[{"article_processing_charge":"No","arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"isi":1,"year":"2015","author":[{"first_name":"Liang","full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi"},{"last_name":"Rampp","full_name":"Rampp, Markus","first_name":"Markus"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"date_updated":"2025-09-22T14:31:33Z","scopus_import":"1","type":"journal_article","volume":106,"department":[{"_id":"BjHo"}],"intvolume":" 106","publisher":"Elsevier","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"quality_controlled":"1","date_published":"2015-01-01T00:00:00Z","publication":"Computers and Fluids","citation":{"ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” Computers and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publication_status":"published","oa_version":"Preprint","fulldoi":"https://doi.org/10.1016/j.compfluid.2014.09.021","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","_id":"2030","language":[{"iso":"eng"}],"doi":"10.1016/j.compfluid.2014.09.021","page":"1 - 11","external_id":{"arxiv":["1311.2481"],"isi":["000346213200001"]},"oa":1,"issue":"1","month":"01","publist_id":"5042","date_created":"2018-12-11T11:55:18Z","status":"public"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"citation":{"ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics. Springer, 2015. https://doi.org/10.1007/s10208-014-9223-y.","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","apa":"Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:10.1007/s10208-014-9223-y."},"file_date_updated":"2020-07-14T12:45:26Z","day":"01","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","title":"The persistent homology of a self-map","fulldoi":"https://doi.org/10.1007/s10208-014-9223-y","_id":"2035","doi":"10.1007/s10208-014-9223-y","language":[{"iso":"eng"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000360862900004"]},"page":"1213 - 1244","oa":1,"month":"10","issue":"5","publist_id":"5022","date_created":"2018-12-11T11:55:20Z","status":"public","file":[{"date_created":"2018-12-12T10:08:10Z","access_level":"open_access","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","relation":"main_file","date_updated":"2020-07-14T12:45:26Z","content_type":"application/pdf","checksum":"3566f3a8b0c1bc550e62914a88c584ff","creator":"system","file_size":1317546,"file_id":"4670"}],"article_processing_charge":"No","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","year":"2015","date_updated":"2025-09-23T14:08:54Z","author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski","orcid":"0000-0002-3536-9866"},{"last_name":"Mrozek","first_name":"Marian","full_name":"Mrozek, Marian"}],"isi":1,"department":[{"_id":"HeEd"}],"volume":15,"type":"journal_article","scopus_import":"1","publisher":"Springer","intvolume":" 15","abstract":[{"lang":"eng","text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n"}],"license":"https://creativecommons.org/licenses/by/4.0/","has_accepted_license":"1","ddc":["000"],"quality_controlled":"1","date_published":"2015-10-01T00:00:00Z","publication":"Foundations of Computational Mathematics","pubrep_id":"486"},{"volume":60,"type":"conference","year":"2015","author":[{"full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","orcid":"0000-0001-8223-8896","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"Can","full_name":"Zhang, Can","last_name":"Zhang"},{"full_name":"Naibert, Tyler","first_name":"Tyler","last_name":"Naibert"},{"first_name":"James","full_name":"Eckstein, James","last_name":"Eckstein"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"date_updated":"2022-02-08T10:42:53Z","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR15/Event/238442"}],"extern":"1","article_processing_charge":"No","date_published":"2015-03-01T00:00:00Z","publication":"APS March Meeting 2015","quality_controlled":"1","abstract":[{"text":"The study of fluxoid states and fluxoid dynamics in mesoscopic iron-based superconducting rings is valuable for characterizing the basic properties of the superconductor, and may also provide important insight into the superconducting paring symmetry. We report the fabrications of micron-sized rings and disks from thin films of Fe(Se, Te) grown by molecular beam epitaxy. In order to study fluxoid states in rings we developed a custom-tailored version of magnetic force microscopy (MFM). This technique has a number of qualitative advantages for working with mesoscopic superconducting samples in comparison to the conventional MFM and other imaging techniques. We observed metastable fluxoid states in rings of different sizes. Thermally activated fluxoid dynamics of these states was studied and modeled. In addition, we found different regimes of interaction between Fe(Se, Te) ring and MFM tip which are explained. Possibilities of the existence of exotic vortex states and proposals for experiments to test the symmetry of the superconducting order parameter in iron based superconductors are analyzed.","lang":"eng"}],"publisher":"American Physical Society","conference":{"end_date":"2015-03-06","name":"APS: American Physical Society","location":"San Antonio, TX, United States","start_date":"2015-03-02"},"intvolume":" 60","title":"Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy","article_number":"G16.00009","_id":"10748","oa_version":"Published Version","publication_status":"published","day":"01","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, and R. Budakian, “Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy,” in APS March Meeting 2015, San Antonio, TX, United States, 2015, vol. 60, no. 1.","apa":"Polshyn, H., Zhang, C., Naibert, T., Eckstein, J., & Budakian, R. (2015). Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In APS March Meeting 2015 (Vol. 60). San Antonio, TX, United States: American Physical Society.","mla":"Polshyn, Hryhoriy, et al. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” APS March Meeting 2015, vol. 60, no. 1, G16.00009, American Physical Society, 2015.","short":"H. Polshyn, C. Zhang, T. Naibert, J. Eckstein, R. Budakian, in:, APS March Meeting 2015, American Physical Society, 2015.","ista":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. 2015. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. APS March Meeting 2015. APS: American Physical Society, Bulletin of the American Physical Society, vol. 60, G16.00009.","ama":"Polshyn H, Zhang C, Naibert T, Eckstein J, Budakian R. Study of Fe (Se, Te) micron-sized rings by magnetic force microscopy. In: APS March Meeting 2015. Vol 60. American Physical Society; 2015.","chicago":"Polshyn, Hryhoriy, Can Zhang, Tyler Naibert, James Eckstein, and Raffi Budakian. “Study of Fe (Se, Te) Micron-Sized Rings by Magnetic Force Microscopy.” In APS March Meeting 2015, Vol. 60. American Physical Society, 2015."},"publication_identifier":{"issn":["0003-0503"]},"date_created":"2022-02-08T10:17:09Z","status":"public","month":"03","alternative_title":["Bulletin of the American Physical Society"],"issue":"1","oa":1,"language":[{"iso":"eng"}]},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.3389/fenvs.2015.00042","publication_identifier":{"issn":["2296-665X"]},"date_created":"2022-02-25T11:42:25Z","status":"public","file":[{"date_created":"2022-02-25T11:55:26Z","file_name":"2015_FrontiersEnvironmScience_Parise.pdf","access_level":"open_access","relation":"main_file","date_updated":"2022-02-25T11:55:26Z","content_type":"application/pdf","checksum":"26c222487564e1be02a11d688d6f769d","file_size":1371201,"creator":"dernst","success":1,"file_id":"10795"}],"month":"06","day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Environmental Science"],"citation":{"ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.","apa":"Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015."},"ec_funded":1,"file_date_updated":"2022-02-25T11:55:26Z","fulldoi":"https://doi.org/10.3389/fenvs.2015.00042","article_number":"42","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","_id":"10794","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_status":"published","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"publisher":"Frontiers","intvolume":" 3","date_published":"2015-06-10T00:00:00Z","publication":"Frontiers in Environmental Science","corr_author":"1","has_accepted_license":"1","ddc":["000","570"],"quality_controlled":"1","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","article_processing_charge":"No","volume":3,"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"scopus_import":"1","type":"journal_article","year":"2015","author":[{"last_name":"Parise","full_name":"Parise, Francesca","first_name":"Francesca"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"},{"first_name":"Jakob","full_name":"Ruess, Jakob","last_name":"Ruess","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T06:50:01Z"},{"publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","OA_place":"publisher","date_published":"2015-01-01T00:00:00Z","corr_author":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy)."}],"publisher":"SIAM","intvolume":" 2015","conference":{"start_date":"2015-01-04","location":"San Diego, CA, United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2015-01-06"},"volume":2015,"department":[{"_id":"KrCh"}],"scopus_import":"1","type":"conference","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"}],"date_updated":"2025-06-26T06:54:08Z","year":"2015","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1409.6690","open_access":"1"}],"arxiv":1,"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","article_processing_charge":"No","status":"public","publication_identifier":{"isbn":["978-161197374-7"]},"date_created":"2022-02-25T12:18:43Z","month":"01","issue":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"page":"1018-1029","external_id":{"arxiv":["1409.6690"]},"doi":"10.1137/1.9781611973730.69","language":[{"iso":"eng"}],"_id":"10796","title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","fulldoi":"https://doi.org/10.1137/1.9781611973730.69","oa_version":"Preprint","publication_status":"published","OA_type":"green","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chatterjee, K., & Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. https://doi.org/10.1137/1.9781611973730.69","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:10.1137/1.9781611973730.69.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2015:1018–29. SIAM, 2015. https://doi.org/10.1137/1.9781611973730.69.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. Vol 2015. SIAM; 2015:1018-1029. doi:10.1137/1.9781611973730.69","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029."},"ec_funded":1},{"date_published":"2015-12-10T00:00:00Z","publication":"Molecular Ecology","quality_controlled":"1","abstract":[{"lang":"eng","text":"Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long‐term studies across Europe and consequently are considered an ecological ‘model organism’. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long‐term study populations of great tits—one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population‐specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population‐specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free‐living populations."}],"publisher":"Wiley","intvolume":" 24","volume":24,"type":"journal_article","year":"2015","date_updated":"2021-01-12T08:15:12Z","author":[{"last_name":"Santure","first_name":"Anna W.","full_name":"Santure, Anna W."},{"last_name":"Poissant","full_name":"Poissant, Jocelyn","first_name":"Jocelyn"},{"full_name":"De Cauwer, Isabelle","first_name":"Isabelle","last_name":"De Cauwer"},{"last_name":"van Oers","full_name":"van Oers, Kees","first_name":"Kees"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"full_name":"Quinn, John L.","first_name":"John L.","last_name":"Quinn"},{"last_name":"Groenen","first_name":"Martien A. M.","full_name":"Groenen, Martien A. M."},{"full_name":"Visser, Marcel E.","first_name":"Marcel E.","last_name":"Visser"},{"first_name":"Ben C.","full_name":"Sheldon, Ben C.","last_name":"Sheldon"},{"full_name":"Slate, Jon","first_name":"Jon","last_name":"Slate"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.13452"}],"extern":"1","article_processing_charge":"No","publication_identifier":{"issn":["0962-1083"]},"date_created":"2020-04-30T10:51:01Z","status":"public","month":"12","page":"6148-6162","oa":1,"language":[{"iso":"eng"}],"article_type":"original","doi":"10.1111/mec.13452","fulldoi":"https://doi.org/10.1111/mec.13452","title":"Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations","_id":"7739","oa_version":"Published Version","publication_status":"published","day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. W. Santure et al., “Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations,” Molecular Ecology, vol. 24. Wiley, pp. 6148–6162, 2015.","apa":"Santure, A. W., Poissant, J., De Cauwer, I., van Oers, K., Robinson, M. R., Quinn, J. L., … Slate, J. (2015). Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.13452","mla":"Santure, Anna W., et al. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology, vol. 24, Wiley, 2015, pp. 6148–62, doi:10.1111/mec.13452.","short":"A.W. Santure, J. Poissant, I. De Cauwer, K. van Oers, M.R. Robinson, J.L. Quinn, M.A.M. Groenen, M.E. Visser, B.C. Sheldon, J. Slate, Molecular Ecology 24 (2015) 6148–6162.","ista":"Santure AW, Poissant J, De Cauwer I, van Oers K, Robinson MR, Quinn JL, Groenen MAM, Visser ME, Sheldon BC, Slate J. 2015. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 24, 6148–6162.","chicago":"Santure, Anna W., Jocelyn Poissant, Isabelle De Cauwer, Kees van Oers, Matthew Richard Robinson, John L. Quinn, Martien A. M. Groenen, Marcel E. Visser, Ben C. Sheldon, and Jon Slate. “Replicated Analysis of the Genetic Architecture of Quantitative Traits in Two Wild Great Tit Populations.” Molecular Ecology. Wiley, 2015. https://doi.org/10.1111/mec.13452.","ama":"Santure AW, Poissant J, De Cauwer I, et al. Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations. Molecular Ecology. 2015;24:6148-6162. doi:10.1111/mec.13452"}},{"article_processing_charge":"No","extern":"1","type":"journal_article","volume":282,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rspb.2015.0689"}],"author":[{"first_name":"Mark James","full_name":"Adams, Mark James","last_name":"Adams"},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"},{"full_name":"Mannarelli, Maria-Elena","first_name":"Maria-Elena","last_name":"Mannarelli"},{"last_name":"Hatchwell","full_name":"Hatchwell, Ben J.","first_name":"Ben J."}],"date_updated":"2021-01-12T08:15:12Z","year":"2015","abstract":[{"text":"Phenotypes expressed in a social context are not only a function of the individual, but can also be shaped by the phenotypes of social partners. These social effects may play a major role in the evolution of cooperative breeding if social partners differ in the quality of care they provide and if individual carers adjust their effort in relation to that of other carers. When applying social effects models to wild study systems, it is also important to explore sources of individual plasticity that could masquerade as social effects. We studied offspring provisioning rates of parents and helpers in a wild population of long-tailed tits Aegithalos caudatus using a quantitative genetic framework to identify these social effects and partition them into genetic, permanent environment and current environment components. Controlling for other effects, individuals were consistent in their provisioning effort at a given nest, but adjusted their effort based on who was in their social group, indicating the presence of social effects. However, these social effects differed between years and social contexts, indicating a current environment effect, rather than indicating a genetic or permanent environment effect. While this study reveals the importance of examining environmental and genetic sources of social effects, the framework we present is entirely general, enabling a greater understanding of potentially important social effects within any ecological population.","lang":"eng"}],"intvolume":" 282","publisher":"The Royal Society","publication":"Proceedings of the Royal Society B: Biological Sciences","date_published":"2015-07-07T00:00:00Z","quality_controlled":"1","day":"07","citation":{"ista":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. 2015. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 282(1810), 20150689.","ama":"Adams MJ, Robinson MR, Mannarelli M-E, Hatchwell BJ. Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. 2015;282(1810). doi:10.1098/rspb.2015.0689","chicago":"Adams, Mark James, Matthew Richard Robinson, Maria-Elena Mannarelli, and Ben J. Hatchwell. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2015. https://doi.org/10.1098/rspb.2015.0689.","ieee":"M. J. Adams, M. R. Robinson, M.-E. Mannarelli, and B. J. Hatchwell, “Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird,” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810. The Royal Society, 2015.","apa":"Adams, M. J., Robinson, M. R., Mannarelli, M.-E., & Hatchwell, B. J. (2015). Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2015.0689","mla":"Adams, Mark James, et al. “Social Genetic and Social Environment Effects on Parental and Helper Care in a Cooperatively Breeding Bird.” Proceedings of the Royal Society B: Biological Sciences, vol. 282, no. 1810, 20150689, The Royal Society, 2015, doi:10.1098/rspb.2015.0689.","short":"M.J. Adams, M.R. Robinson, M.-E. Mannarelli, B.J. Hatchwell, Proceedings of the Royal Society B: Biological Sciences 282 (2015)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7741","title":"Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird","fulldoi":"https://doi.org/10.1098/rspb.2015.0689","article_number":"20150689","publication_status":"published","pmid":1,"oa_version":"Published Version","oa":1,"external_id":{"pmid":["26063846"]},"doi":"10.1098/rspb.2015.0689","article_type":"original","language":[{"iso":"eng"}],"status":"public","date_created":"2020-04-30T10:58:07Z","publication_identifier":{"issn":["0962-8452","1471-2954"]},"issue":"1810","month":"07"},{"year":"2015","oa_version":"None","author":[{"first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813"},{"first_name":"Gibran","full_name":"Hemani, Gibran","last_name":"Hemani"},{"last_name":"Medina-Gomez","full_name":"Medina-Gomez, Carolina","first_name":"Carolina"},{"first_name":"Massimo","full_name":"Mezzavilla, Massimo","last_name":"Mezzavilla"},{"last_name":"Esko","full_name":"Esko, Tonu","first_name":"Tonu"},{"last_name":"Shakhbazov","first_name":"Konstantin","full_name":"Shakhbazov, Konstantin"},{"first_name":"Joseph E","full_name":"Powell, Joseph E","last_name":"Powell"},{"last_name":"Vinkhuyzen","first_name":"Anna","full_name":"Vinkhuyzen, Anna"},{"last_name":"Berndt","full_name":"Berndt, Sonja I","first_name":"Sonja I"},{"first_name":"Stefan","full_name":"Gustafsson, Stefan","last_name":"Gustafsson"},{"first_name":"Anne E","full_name":"Justice, Anne E","last_name":"Justice"},{"last_name":"Kahali","first_name":"Bratati","full_name":"Kahali, Bratati"},{"first_name":"Adam E","full_name":"Locke, Adam E","last_name":"Locke"},{"last_name":"Pers","full_name":"Pers, Tune H","first_name":"Tune H"},{"last_name":"Vedantam","first_name":"Sailaja","full_name":"Vedantam, Sailaja"},{"last_name":"Wood","full_name":"Wood, Andrew R","first_name":"Andrew R"},{"full_name":"van Rheenen, Wouter","first_name":"Wouter","last_name":"van Rheenen"},{"last_name":"Andreassen","first_name":"Ole A","full_name":"Andreassen, Ole A"},{"full_name":"Gasparini, Paolo","first_name":"Paolo","last_name":"Gasparini"},{"last_name":"Metspalu","full_name":"Metspalu, Andres","first_name":"Andres"},{"last_name":"Berg","first_name":"Leonard H van den","full_name":"Berg, Leonard H van den"},{"full_name":"Veldink, Jan H","first_name":"Jan H","last_name":"Veldink"},{"last_name":"Rivadeneira","first_name":"Fernando","full_name":"Rivadeneira, Fernando"},{"full_name":"Werge, Thomas M","first_name":"Thomas M","last_name":"Werge"},{"last_name":"Abecasis","first_name":"Goncalo R","full_name":"Abecasis, Goncalo R"},{"last_name":"Boomsma","first_name":"Dorret I","full_name":"Boomsma, Dorret I"},{"full_name":"Chasman, Daniel I","first_name":"Daniel I","last_name":"Chasman"},{"full_name":"de Geus, Eco J C","first_name":"Eco J C","last_name":"de Geus"},{"full_name":"Frayling, Timothy M","first_name":"Timothy M","last_name":"Frayling"},{"last_name":"Hirschhorn","first_name":"Joel N","full_name":"Hirschhorn, Joel N"},{"last_name":"Hottenga","full_name":"Hottenga, Jouke Jan","first_name":"Jouke Jan"},{"first_name":"Erik","full_name":"Ingelsson, Erik","last_name":"Ingelsson"},{"last_name":"Loos","full_name":"Loos, Ruth J F","first_name":"Ruth J F"},{"first_name":"Patrik K E","full_name":"Magnusson, Patrik K E","last_name":"Magnusson"},{"last_name":"Martin","first_name":"Nicholas G","full_name":"Martin, Nicholas G"},{"first_name":"Grant W","full_name":"Montgomery, Grant W","last_name":"Montgomery"},{"last_name":"North","full_name":"North, Kari E","first_name":"Kari E"},{"last_name":"Pedersen","first_name":"Nancy L","full_name":"Pedersen, Nancy L"},{"last_name":"Spector","full_name":"Spector, Timothy D","first_name":"Timothy D"},{"first_name":"Elizabeth K","full_name":"Speliotes, Elizabeth K","last_name":"Speliotes"},{"full_name":"Goddard, Michael E","first_name":"Michael E","last_name":"Goddard"},{"first_name":"Jian","full_name":"Yang, Jian","last_name":"Yang"},{"full_name":"Visscher, Peter M","first_name":"Peter M","last_name":"Visscher"}],"date_updated":"2021-01-12T08:15:13Z","publication_status":"published","volume":47,"fulldoi":"https://doi.org/10.1038/ng.3401","title":"Population genetic differentiation of height and body mass index across Europe","type":"journal_article","_id":"7742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Robinson, Matthew Richard, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics, vol. 47, no. 11, Springer Nature, 2015, pp. 1357–62, doi:10.1038/ng.3401.","short":"M.R. Robinson, G. Hemani, C. Medina-Gomez, M. Mezzavilla, T. Esko, K. Shakhbazov, J.E. Powell, A. Vinkhuyzen, S.I. Berndt, S. Gustafsson, A.E. Justice, B. Kahali, A.E. Locke, T.H. Pers, S. Vedantam, A.R. Wood, W. van Rheenen, O.A. Andreassen, P. Gasparini, A. Metspalu, L.H. van den Berg, J.H. Veldink, F. Rivadeneira, T.M. Werge, G.R. Abecasis, D.I. Boomsma, D.I. Chasman, E.J.C. de Geus, T.M. Frayling, J.N. Hirschhorn, J.J. Hottenga, E. Ingelsson, R.J.F. Loos, P.K.E. Magnusson, N.G. Martin, G.W. Montgomery, K.E. North, N.L. Pedersen, T.D. Spector, E.K. Speliotes, M.E. Goddard, J. Yang, P.M. Visscher, Nature Genetics 47 (2015) 1357–1362.","ieee":"M. R. Robinson et al., “Population genetic differentiation of height and body mass index across Europe,” Nature Genetics, vol. 47, no. 11. Springer Nature, pp. 1357–1362, 2015.","apa":"Robinson, M. R., Hemani, G., Medina-Gomez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., … Visscher, P. M. (2015). Population genetic differentiation of height and body mass index across Europe. Nature Genetics. Springer Nature. https://doi.org/10.1038/ng.3401","ista":"Robinson MR, Hemani G, Medina-Gomez C, Mezzavilla M, Esko T, Shakhbazov K, Powell JE, Vinkhuyzen A, Berndt SI, Gustafsson S, Justice AE, Kahali B, Locke AE, Pers TH, Vedantam S, Wood AR, van Rheenen W, Andreassen OA, Gasparini P, Metspalu A, Berg LH van den, Veldink JH, Rivadeneira F, Werge TM, Abecasis GR, Boomsma DI, Chasman DI, de Geus EJC, Frayling TM, Hirschhorn JN, Hottenga JJ, Ingelsson E, Loos RJF, Magnusson PKE, Martin NG, Montgomery GW, North KE, Pedersen NL, Spector TD, Speliotes EK, Goddard ME, Yang J, Visscher PM. 2015. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 47(11), 1357–1362.","ama":"Robinson MR, Hemani G, Medina-Gomez C, et al. Population genetic differentiation of height and body mass index across Europe. Nature Genetics. 2015;47(11):1357-1362. doi:10.1038/ng.3401","chicago":"Robinson, Matthew Richard, Gibran Hemani, Carolina Medina-Gomez, Massimo Mezzavilla, Tonu Esko, Konstantin Shakhbazov, Joseph E Powell, et al. “Population Genetic Differentiation of Height and Body Mass Index across Europe.” Nature Genetics. Springer Nature, 2015. https://doi.org/10.1038/ng.3401."},"article_processing_charge":"No","day":"14","extern":"1","month":"09","quality_controlled":"1","issue":"11","publication_identifier":{"issn":["1061-4036","1546-1718"]},"date_created":"2020-04-30T10:58:23Z","date_published":"2015-09-14T00:00:00Z","publication":"Nature Genetics","status":"public","article_type":"original","doi":"10.1038/ng.3401","language":[{"iso":"eng"}],"publisher":"Springer Nature","intvolume":" 47","page":"1357-1362","abstract":[{"lang":"eng","text":"Across-nation differences in the mean values for complex traits are common1,2,3,4,5,6,7,8, but the reasons for these differences are unknown. Here we find that many independent loci contribute to population genetic differences in height and body mass index (BMI) in 9,416 individuals across 14 European countries. Using discovery data on over 250,000 individuals and unbiased effect size estimates from 17,500 sibling pairs, we estimate that 24% (95% credible interval (CI) = 9%, 41%) and 8% (95% CI = 4%, 16%) of the captured additive genetic variance for height and BMI, respectively, reflect population genetic differences. Population genetic divergence differed significantly from that in a null model (height, P < 3.94 × 10−8; BMI, P < 5.95 × 10−4), and we find an among-population genetic correlation for tall and slender individuals (r = −0.80, 95% CI = −0.95, −0.60), consistent with correlated selection for both phenotypes. Observed differences in height among populations reflected the predicted genetic means (r = 0.51; P < 0.001), but environmental differences across Europe masked genetic differentiation for BMI (P < 0.58)."}]},{"type":"conference","scopus_import":"1","date_updated":"2026-05-18T12:40:58Z","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Kopinsky","full_name":"Kopinsky, Justin","first_name":"Justin"},{"last_name":"Li","first_name":"Jerry","full_name":"Li, Jerry"},{"last_name":"Shavit","full_name":"Shavit, Nir","first_name":"Nir"}],"year":"2015","extern":"1","article_processing_charge":"No","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\r\nand Intel corporations.","publication":"Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","date_published":"2015-01-24T00:00:00Z","quality_controlled":"1","abstract":[{"text":"High-performance concurrent priority queues are essential for applications such as task scheduling and discrete event simulation. Unfortunately, even the best performing implementations do not scale past a number of threads in the single digits. This is because of the sequential bottleneck in accessing the elements at the head of the queue in order to perform a DeleteMin operation. In this paper, we present the SprayList, a scalable priority queue with relaxed ordering semantics. Starting from a non-blocking SkipList, the main innovation behind our design is that the DeleteMin operations avoid a sequential bottleneck by "spraying" themselves onto the head of the SkipList list in a coordinated fashion. The spraying is implemented using a carefully designed random walk, so that DeleteMin returns an element among the first O(plog3p) in the list, with high probability, where p is the number of threads. We prove that the running time of a DeleteMin operation is O(log3p), with high probability, independent of the size of the list. Our experiments show that the relaxed semantics allow the data structure to scale for high thread counts, comparable to a classic unordered SkipList. Furthermore, we observe that, for reasonably parallel workloads, the scalability benefits of relaxation considerably outweigh the additional work due to out-of-order execution.","lang":"eng"}],"publisher":"ACM","conference":{"start_date":"2015-02-07","location":"San Francisco, CA, United States","name":"PPoPP: Principles and Practice of Parallel Pogramming","end_date":"2015-02-11"},"_id":"776","title":"The SprayList: A scalable relaxed priority queue","fulldoi":"https://doi.org/10.1145/2688500.2688523","oa_version":"None","OA_type":"closed access","publication_status":"published","day":"24","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Alistarh, Dan-Adrian, et al. “The SprayList: A Scalable Relaxed Priority Queue.” Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, 2015, pp. 11–20, doi:10.1145/2688500.2688523.","short":"D.-A. Alistarh, J. Kopinsky, J. Li, N. Shavit, in:, Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, ACM, 2015, pp. 11–20.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., & Shavit, N. (2015). The SprayList: A scalable relaxed priority queue. In Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 11–20). San Francisco, CA, United States: ACM. https://doi.org/10.1145/2688500.2688523","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and N. Shavit, “The SprayList: A scalable relaxed priority queue,” in Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Francisco, CA, United States, 2015, pp. 11–20.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Nir Shavit. “The SprayList: A Scalable Relaxed Priority Queue.” In Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 11–20. ACM, 2015. https://doi.org/10.1145/2688500.2688523.","ama":"Alistarh D-A, Kopinsky J, Li J, Shavit N. The SprayList: A scalable relaxed priority queue. In: Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. ACM; 2015:11-20. doi:10.1145/2688500.2688523","ista":"Alistarh D-A, Kopinsky J, Li J, Shavit N. 2015. The SprayList: A scalable relaxed priority queue. Proceedings of the 20th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Principles and Practice of Parallel Pogramming, 11–20."},"status":"public","date_created":"2018-12-11T11:48:26Z","publist_id":"6878","publication_identifier":{"isbn":["9781450332057"]},"month":"01","page":"11 - 20","language":[{"iso":"eng"}],"doi":"10.1145/2688500.2688523"},{"month":"06","issue":"22","quality_controlled":"1","date_created":"2020-04-30T11:41:08Z","publication_identifier":{"issn":["0031-9007","1079-7114"]},"date_published":"2015-06-04T00:00:00Z","publication":"Physical Review Letters","status":"public","language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.114.225501","article_type":"original","publisher":"American Physical Society","intvolume":" 114","abstract":[{"text":"We introduce a principle unique to disordered solids wherein the contribution of any bond to one global perturbation is uncorrelated with its contribution to another. Coupled with sufficient variability in the contributions of different bonds, this “independent bond-level response” paves the way for the design of real materials with unusual and exquisitely tuned properties. To illustrate this, we choose two global perturbations: compression and shear. By applying a bond removal procedure that is both simple and experimentally relevant to remove a very small fraction of bonds, we can drive disordered spring networks to both the incompressible and completely auxetic limits of mechanical behavior.","lang":"eng"}],"year":"2015","oa_version":"None","author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"},{"first_name":"Andrea J.","full_name":"Liu, Andrea J.","last_name":"Liu"},{"last_name":"Nagel","full_name":"Nagel, Sidney R.","first_name":"Sidney R."}],"date_updated":"2021-01-12T08:15:23Z","publication_status":"published","volume":114,"article_number":"225501","fulldoi":"https://doi.org/10.1103/physrevlett.114.225501","title":"The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior","type":"journal_article","_id":"7765","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/physrevlett.114.225501.","ama":"Goodrich CP, Liu AJ, Nagel SR. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 2015;114(22). doi:10.1103/physrevlett.114.225501","ista":"Goodrich CP, Liu AJ, Nagel SR. 2015. The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. 114(22), 225501.","apa":"Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.114.225501","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “The principle of independent bond-level response: Tuning by pruning to exploit disorder for global behavior,” Physical Review Letters, vol. 114, no. 22. American Physical Society, 2015.","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 114 (2015).","mla":"Goodrich, Carl Peter, et al. “The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior.” Physical Review Letters, vol. 114, no. 22, 225501, American Physical Society, 2015, doi:10.1103/physrevlett.114.225501."},"day":"04","extern":"1","article_processing_charge":"No"},{"date_created":"2020-04-30T11:41:23Z","publication_identifier":{"issn":["1744-683X","1744-6848"]},"date_published":"2015-02-15T00:00:00Z","publication":"Soft Matter","status":"public","month":"02","issue":"14","quality_controlled":"1","page":"2745-2751","abstract":[{"text":"We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale ω*. This frequency is controlled by ΔZ = 〈Z〉 − 2d, the difference between the average coordination of the spheres and twice the spatial dimension, d, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below ω*. The total number of these low-frequency surface modes is controlled by ΔZ, and the profile of their decay into the bulk has two characteristic length scales, which diverge as ΔZ−1/2 and ΔZ−1 as the jamming transition is approached.","lang":"eng"}],"article_type":"original","doi":"10.1039/c4sm02905d","language":[{"iso":"eng"}],"publisher":"Royal Society of Chemistry","intvolume":" 11","volume":11,"title":"Disordered surface vibrations in jammed sphere packings","fulldoi":"https://doi.org/10.1039/c4sm02905d","type":"journal_article","_id":"7766","year":"2015","date_updated":"2021-01-12T08:15:23Z","oa_version":"None","author":[{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"last_name":"Nagel","full_name":"Nagel, Sidney R.","first_name":"Sidney R."}],"publication_status":"published","extern":"1","article_processing_charge":"No","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sussman, Daniel M., et al. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter, vol. 11, no. 14, Royal Society of Chemistry, 2015, pp. 2745–51, doi:10.1039/c4sm02905d.","short":"D.M. Sussman, C.P. Goodrich, A.J. Liu, S.R. Nagel, Soft Matter 11 (2015) 2745–2751.","apa":"Sussman, D. M., Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2015). Disordered surface vibrations in jammed sphere packings. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c4sm02905d","ieee":"D. M. Sussman, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Disordered surface vibrations in jammed sphere packings,” Soft Matter, vol. 11, no. 14. Royal Society of Chemistry, pp. 2745–2751, 2015.","ama":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. Disordered surface vibrations in jammed sphere packings. Soft Matter. 2015;11(14):2745-2751. doi:10.1039/c4sm02905d","chicago":"Sussman, Daniel M., Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Disordered Surface Vibrations in Jammed Sphere Packings.” Soft Matter. Royal Society of Chemistry, 2015. https://doi.org/10.1039/c4sm02905d.","ista":"Sussman DM, Goodrich CP, Liu AJ, Nagel SR. 2015. Disordered surface vibrations in jammed sphere packings. Soft Matter. 11(14), 2745–2751."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Drongelen, Ruben van, Anshuman Pal, Carl Peter Goodrich, and Timon Idema. “Collective Dynamics of Soft Active Particles.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/physreve.91.032706.","ama":"van Drongelen R, Pal A, Goodrich CP, Idema T. Collective dynamics of soft active particles. Physical Review E. 2015;91(3). doi:10.1103/physreve.91.032706","ista":"van Drongelen R, Pal A, Goodrich CP, Idema T. 2015. Collective dynamics of soft active particles. Physical Review E. 91(3), 032706.","mla":"van Drongelen, Ruben, et al. “Collective Dynamics of Soft Active Particles.” Physical Review E, vol. 91, no. 3, 032706, American Physical Society, 2015, doi:10.1103/physreve.91.032706.","short":"R. van Drongelen, A. Pal, C.P. Goodrich, T. Idema, Physical Review E 91 (2015).","apa":"van Drongelen, R., Pal, A., Goodrich, C. P., & Idema, T. (2015). Collective dynamics of soft active particles. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.91.032706","ieee":"R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema, “Collective dynamics of soft active particles,” Physical Review E, vol. 91, no. 3. American Physical Society, 2015."},"extern":"1","day":"01","article_processing_charge":"No","year":"2015","date_updated":"2021-01-12T08:15:24Z","oa_version":"None","author":[{"last_name":"van Drongelen","first_name":"Ruben","full_name":"van Drongelen, Ruben"},{"last_name":"Pal","first_name":"Anshuman","full_name":"Pal, Anshuman"},{"full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","orcid":"0000-0002-1307-5074","last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425"},{"last_name":"Idema","full_name":"Idema, Timon","first_name":"Timon"}],"publication_status":"published","volume":91,"fulldoi":"https://doi.org/10.1103/physreve.91.032706","title":"Collective dynamics of soft active particles","article_number":"032706","_id":"7767","type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","doi":"10.1103/physreve.91.032706","publisher":"American Physical Society","intvolume":" 91","abstract":[{"text":"We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength of these interactions leads to migrating swarms, rotating swarms, and jammed swarms, as well as swarms that exhibit run-and-tumble motion, alternating between migration and either rotating or jammed states. Interestingly, although a migrating swarm moves slower than an individual particle, the diffusion constant can be up to three orders of magnitude larger, suggesting that collective motion can be highly advantageous, for example, when searching for food.","lang":"eng"}],"month":"03","quality_controlled":"1","issue":"3","date_published":"2015-03-01T00:00:00Z","publication_identifier":{"issn":["1539-3755","1550-2376"]},"date_created":"2020-04-30T11:41:38Z","status":"public","publication":"Physical Review E"},{"language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems","conference":{"location":"Montréal, Canada","start_date":"2015-12-07","end_date":"2015-12-12","name":"NIPS: Neural Information Processing Systems"},"page":"1900 - 1908","abstract":[{"text":"In many applications, the data is of rich structure that can be represented by a hypergraph, where the data items are represented by vertices and the associations among items are represented by hyperedges. Equivalently, we are given an input bipartite graph with two types of vertices: items, and associations (which we refer to as topics). We consider the problem of partitioning the set of items into a given number of components such that the maximum number of topics covered by a component is minimized. This is a clustering problem with various applications, e.g. partitioning of a set of information objects such as documents, images, and videos, and load balancing in the context of modern computation platforms.Inthis paper, we focus on the streaming computation model for this problem, in which items arrive online one at a time and each item must be assigned irrevocably to a component at its arrival time. Motivated by scalability requirements, we focus on the class of streaming computation algorithms with memory limited to be at most linear in the number of components. We show that a greedy assignment strategy is able to recover a hidden co-clustering of items under a natural set of recovery conditions. We also report results of an extensive empirical evaluation, which demonstrate that this greedy strategy yields superior performance when compared with alternative approaches.","lang":"eng"}],"month":"01","publist_id":"6879","date_created":"2018-12-11T11:48:27Z","date_published":"2015-01-01T00:00:00Z","publication_identifier":{"isbn":["9781510825024"]},"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Alistarh D-A, Iglesias J, Vojnović M. 2015. Streaming min-max hypergraph partitioning. NIPS: Neural Information Processing Systems vol. 2015–January, 1900–1908.","chicago":"Alistarh, Dan-Adrian, Jennifer Iglesias, and Milan Vojnović. “Streaming Min-Max Hypergraph Partitioning,” 2015–January:1900–1908. Neural Information Processing Systems, 2015.","ama":"Alistarh D-A, Iglesias J, Vojnović M. Streaming min-max hypergraph partitioning. In: Vol 2015-January. Neural Information Processing Systems; 2015:1900-1908.","mla":"Alistarh, Dan-Adrian, et al. Streaming Min-Max Hypergraph Partitioning. Vol. 2015–January, Neural Information Processing Systems, 2015, pp. 1900–08.","short":"D.-A. Alistarh, J. Iglesias, M. Vojnović, in:, Neural Information Processing Systems, 2015, pp. 1900–1908.","ieee":"D.-A. Alistarh, J. Iglesias, and M. Vojnović, “Streaming min-max hypergraph partitioning,” presented at the NIPS: Neural Information Processing Systems, Montréal, Canada, 2015, vol. 2015–January, pp. 1900–1908.","apa":"Alistarh, D.-A., Iglesias, J., & Vojnović, M. (2015). Streaming min-max hypergraph partitioning (Vol. 2015–January, pp. 1900–1908). Presented at the NIPS: Neural Information Processing Systems, Montréal, Canada: Neural Information Processing Systems."},"article_processing_charge":"No","extern":"1","day":"01","year":"2015","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Iglesias","first_name":"Jennifer","full_name":"Iglesias, Jennifer"},{"full_name":"Vojnović, Milan","first_name":"Milan","last_name":"Vojnović"}],"oa_version":"None","date_updated":"2026-05-19T08:39:02Z","main_file_link":[{"url":"http://papers.nips.cc/paper/5897-streaming-min-max-hypergraph-partitioning"}],"publication_status":"published","volume":"2015-January","title":"Streaming min-max hypergraph partitioning","_id":"777","type":"conference"},{"_id":"7779","type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.1510.08820","title":"Unearthing the anticrystal: Criticality in the linear response of disordered solids","article_number":"1510.08820","OA_type":"green","publication_status":"submitted","main_file_link":[{"url":"https://arxiv.org/abs/1510.08820","open_access":"1"}],"author":[{"last_name":"Goodrich","orcid":"0000-0002-1307-5074","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter"}],"oa_version":"Preprint","date_updated":"2025-06-26T10:26:40Z","year":"2015","arxiv":1,"article_processing_charge":"No","day":"29","extern":"1","citation":{"chicago":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1510.08820.","ama":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. doi:10.48550/arXiv.1510.08820","ista":"Goodrich CP. Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv, 1510.08820.","mla":"Goodrich, Carl Peter. “Unearthing the Anticrystal: Criticality in the Linear Response of Disordered Solids.” ArXiv, 1510.08820, doi:10.48550/arXiv.1510.08820.","short":"C.P. Goodrich, ArXiv (n.d.).","apa":"Goodrich, C. P. (n.d.). Unearthing the anticrystal: Criticality in the linear response of disordered solids. arXiv. https://doi.org/10.48550/arXiv.1510.08820","ieee":"C. P. Goodrich, “Unearthing the anticrystal: Criticality in the linear response of disordered solids,” arXiv. ."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"arXiv","date_created":"2020-04-30T12:16:18Z","date_published":"2015-10-29T00:00:00Z","month":"10","oa":1,"abstract":[{"lang":"eng","text":"The fact that a disordered material is not constrained in its properties in\r\nthe same way as a crystal presents significant and yet largely untapped\r\npotential for novel material design. However, unlike their crystalline\r\ncounterparts, disordered solids are not well understood. One of the primary\r\nobstacles is the lack of a theoretical framework for thinking about disorder\r\nand its relation to mechanical properties. To this end, we study an idealized\r\nsystem of frictionless athermal soft spheres that, when compressed, undergoes a\r\njamming phase transition with diverging length scales and clean power-law\r\nsignatures. This critical point is the cornerstone of a much larger \"jamming\r\nscenario\" that has the potential to provide the essential theoretical\r\nfoundation necessary for a unified understanding of the mechanics of disordered\r\nsolids. We begin by showing that jammed sphere packings have a valid linear\r\nregime despite the presence of \"contact nonlinearities.\" We then investigate\r\nthe critical nature of the transition, focusing on diverging length scales and\r\nfinite-size effects. Next, we argue that jamming plays the same role for\r\ndisordered solids as the perfect crystal plays for crystalline solids. Not only\r\ncan it be considered an idealized starting point for understanding disordered\r\nmaterials, but it can even influence systems that have a relatively high amount\r\nof crystalline order. The behavior of solids can thus be thought of as existing\r\non a spectrum, with the perfect crystal and the jamming transition at opposing\r\nends. Finally, we introduce a new principle wherein the contribution of an\r\nindividual bond to one global property is independent of its contribution to\r\nanother. This principle allows the different global responses of a disordered\r\nsystem to be manipulated independently and provides a great deal of flexibility\r\nin designing materials with unique, textured and tunable properties."}],"external_id":{"arxiv":["1510.08820"]},"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1510.08820"},{"alternative_title":["LNCS"],"month":"01","date_created":"2018-12-11T11:48:27Z","publist_id":"6880","status":"public","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-48653-5_13","external_id":{"arxiv":["1405.5689"]},"page":"185 - 199","oa":1,"publication_status":"published","oa_version":"None","title":"Inherent limitations of hybrid transactional memory","fulldoi":"https://doi.org/10.1007/978-3-662-48653-5_13","_id":"778","citation":{"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.","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:10.1007/978-3-662-48653-5_13","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Petr Kuznetsov, Srivatsan Ravi, and Nir Shavit. “Inherent Limitations of Hybrid Transactional Memory,” 9363:185–99. Springer, 2015. https://doi.org/10.1007/978-3-662-48653-5_13.","short":"D.-A. Alistarh, J. Kopinsky, P. Kuznetsov, S. Ravi, N. Shavit, in:, Springer, 2015, pp. 185–199.","mla":"Alistarh, Dan-Adrian, et al. Inherent Limitations of Hybrid Transactional Memory. Vol. 9363, Springer, 2015, pp. 185–99, doi:10.1007/978-3-662-48653-5_13.","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.","apa":"Alistarh, D.-A., Kopinsky, J., Kuznetsov, P., Ravi, S., & Shavit, N. (2015). Inherent limitations of hybrid transactional memory (Vol. 9363, pp. 185–199). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-662-48653-5_13"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","quality_controlled":"1","date_published":"2015-01-01T00:00:00Z","conference":{"name":"DISC: Distributed Computing"},"intvolume":" 9363","publisher":"Springer","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."}],"main_file_link":[{"url":"https://arxiv.org/abs/1405.5689","open_access":"1"}],"year":"2015","author":[{"orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Kopinsky, Justin","first_name":"Justin","last_name":"Kopinsky"},{"last_name":"Kuznetsov","first_name":"Petr","full_name":"Kuznetsov, Petr"},{"full_name":"Ravi, Srivatsan","first_name":"Srivatsan","last_name":"Ravi"},{"last_name":"Shavit","full_name":"Shavit, Nir","first_name":"Nir"}],"date_updated":"2023-02-23T13:17:35Z","type":"conference","volume":9363,"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.","article_processing_charge":"No","extern":"1","arxiv":1},{"month":"06","date_published":"2015-06-13T00:00:00Z","publist_id":"6876","date_created":"2018-12-11T11:48:27Z","status":"public","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"doi":"10.1145/2755573.2755600","language":[{"iso":"eng"}],"publisher":"ACM","page":"123 - 132","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"}],"publication_status":"published","year":"2015","author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Matveev","first_name":"Alexander","full_name":"Matveev, Alexander"},{"full_name":"Leiserson, William","first_name":"William","last_name":"Leiserson"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"}],"date_updated":"2023-02-23T12:35:42Z","oa_version":"None","title":"ThreadScan: Automatic and scalable memory reclamation","fulldoi":"https://doi.org/10.1145/2755573.2755600","_id":"779","type":"conference","volume":"2015-June","related_material":{"record":[{"relation":"later_version","status":"public","id":"6001"}]},"citation":{"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.","apa":"Alistarh, D.-A., Matveev, A., Leiserson, W., & 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. https://doi.org/10.1145/2755573.2755600","mla":"Alistarh, Dan-Adrian, et al. ThreadScan: Automatic and Scalable Memory Reclamation. Vol. 2015–June, ACM, 2015, pp. 123–32, doi:10.1145/2755573.2755600.","short":"D.-A. Alistarh, A. Matveev, W. Leiserson, N. Shavit, in:, ACM, 2015, pp. 123–132.","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. https://doi.org/10.1145/2755573.2755600.","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:10.1145/2755573.2755600"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","extern":"1","article_processing_charge":"No","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."},{"_id":"780","fulldoi":"https://doi.org/10.1007/978-3-662-47666-6_38","title":"Polylogarithmic-time leader election in population protocols","oa_version":"Preprint","OA_type":"green","publication_status":"published","day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Alistarh, D.-A., & Gelashvili, R. (2015). Polylogarithmic-time leader election in population protocols. In Proceedings of the 42nd International Colloquium on Automata, Languages and Programming (Vol. 9135, pp. 479–491). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_38","ieee":"D.-A. Alistarh and R. Gelashvili, “Polylogarithmic-time leader election in population protocols,” in Proceedings of the 42nd International Colloquium on Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9135, pp. 479–491.","short":"D.-A. Alistarh, R. Gelashvili, in:, Proceedings of the 42nd International Colloquium on Automata, Languages and Programming, Springer Nature, 2015, pp. 479–491.","mla":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols.” Proceedings of the 42nd International Colloquium on Automata, Languages and Programming, vol. 9135, Springer Nature, 2015, pp. 479–91, doi:10.1007/978-3-662-47666-6_38.","chicago":"Alistarh, Dan-Adrian, and Rati Gelashvili. “Polylogarithmic-Time Leader Election in Population Protocols.” In Proceedings of the 42nd International Colloquium on Automata, Languages and Programming, 9135:479–91. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_38.","ama":"Alistarh D-A, Gelashvili R. Polylogarithmic-time leader election in population protocols. In: Proceedings of the 42nd International Colloquium on Automata, Languages and Programming. Vol 9135. Springer Nature; 2015:479-491. doi:10.1007/978-3-662-47666-6_38","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."},"status":"public","date_created":"2018-12-11T11:48:28Z","publication_identifier":{"isbn":["9783662476659"],"eisbn":["9783662476666"]},"publist_id":"6877","month":"01","oa":1,"page":"479 - 491","external_id":{"arxiv":["1502.05745"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-47666-6_38","volume":9135,"type":"conference","author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"}],"date_updated":"2026-05-19T13:03:42Z","year":"2015","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.05745"}],"arxiv":1,"article_processing_charge":"No","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.”","extern":"1","publication":"Proceedings of the 42nd International Colloquium on Automata, Languages and Programming","OA_place":"repository","date_published":"2015-01-01T00:00:00Z","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"}],"publisher":"Springer Nature","conference":{"name":"ICALP: International Colloquium on Automota, Languages and Programming","end_date":"2015-07-10","start_date":"2015-07-06","location":"Kyoto, Japan"},"intvolume":" 9135"},{"volume":"2015-July","title":"Fast and exact majority in population protocols","fulldoi":"https://doi.org/10.1145/2767386.2767429","_id":"781","type":"conference","year":"2015","date_updated":"2023-02-23T13:18:35Z","oa_version":"None","author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"first_name":"Milan","full_name":"Vojnović, Milan","last_name":"Vojnović"}],"publication_status":"published","day":"21","extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Milan Vojnović. “Fast and Exact Majority in Population Protocols,” 2015–July:47–56. ACM, 2015. https://doi.org/10.1145/2767386.2767429.","ama":"Alistarh D-A, Gelashvili R, Vojnović M. Fast and exact majority in population protocols. In: Vol 2015-July. ACM; 2015:47-56. doi:10.1145/2767386.2767429","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.","mla":"Alistarh, Dan-Adrian, et al. Fast and Exact Majority in Population Protocols. Vol. 2015–July, ACM, 2015, pp. 47–56, doi:10.1145/2767386.2767429.","short":"D.-A. Alistarh, R. Gelashvili, M. Vojnović, in:, ACM, 2015, pp. 47–56.","apa":"Alistarh, D.-A., Gelashvili, R., & 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. https://doi.org/10.1145/2767386.2767429","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."},"date_published":"2015-07-21T00:00:00Z","publist_id":"6873","date_created":"2018-12-11T11:48:28Z","status":"public","month":"07","page":"47 - 56","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"}],"language":[{"iso":"eng"}],"doi":"10.1145/2767386.2767429","publisher":"ACM","conference":{"name":"PODC: Principles of Distributed Computing"}},{"day":"21","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ieee":"D.-A. Alistarh, T. Sauerwald, and M. Vojnović, “Lock-Free algorithms under stochastic schedulers,” in Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, New York, NY, United States, 2015, vol. 2015–July, pp. 251–260.","apa":"Alistarh, D.-A., Sauerwald, T., & Vojnović, M. (2015). Lock-Free algorithms under stochastic schedulers. In Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing (Vol. 2015–July, pp. 251–260). New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2767386.2767430","mla":"Alistarh, Dan-Adrian, et al. “Lock-Free Algorithms under Stochastic Schedulers.” Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, vol. 2015–July, Association for Computing Machinery, 2015, pp. 251–60, doi:10.1145/2767386.2767430.","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.","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 Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, 2015–July:251–60. Association for Computing Machinery, 2015. https://doi.org/10.1145/2767386.2767430.","ama":"Alistarh D-A, Sauerwald T, Vojnović M. Lock-Free algorithms under stochastic schedulers. In: Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing. Vol 2015-July. Association for Computing Machinery; 2015:251-260. doi:10.1145/2767386.2767430"},"title":"Lock-Free algorithms under stochastic schedulers","fulldoi":"https://doi.org/10.1145/2767386.2767430","_id":"782","oa_version":"Accepted Version","OA_type":"free access","publication_status":"published","page":"251 - 260","oa":1,"doi":"10.1145/2767386.2767430","language":[{"iso":"eng"}],"publist_id":"6874","date_created":"2018-12-11T11:48:28Z","publication_identifier":{"eisbn":["9781450336178"]},"status":"public","month":"07","extern":"1","article_processing_charge":"No","volume":"2015-July","scopus_import":"1","type":"conference","year":"2015","author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","full_name":"Sauerwald, Thomas","last_name":"Sauerwald"},{"last_name":"Vojnović","first_name":"Milan","full_name":"Vojnović, Milan"}],"date_updated":"2026-05-19T13:21:59Z","main_file_link":[{"url":"http://dx.doi.org/10.1145/2767386.2767430","open_access":"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"}],"publisher":"Association for Computing Machinery","conference":{"location":"New York, NY, United States","start_date":"2015-07-21","end_date":"2015-7-23","name":"PODC: Principles of Distributed Computing"},"date_published":"2015-07-21T00:00:00Z","OA_place":"publisher","publication":"Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing","quality_controlled":"1"},{"main_file_link":[{"url":"https://doi.org/10.1145/2767386.2767420","open_access":"1"}],"author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"last_name":"Vladu","full_name":"Vladu, Adrian","first_name":"Adrian"}],"date_updated":"2026-05-19T13:27:49Z","year":"2015","scopus_import":"1","type":"conference","arxiv":1,"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.","extern":"1","article_processing_charge":"No","quality_controlled":"1","publication":"Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing","OA_place":"publisher","date_published":"2015-07-21T00:00:00Z","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2015-07-23","start_date":"2015-07-21","location":"New York, NY, United States"},"publisher":"Association for Computing Machinery","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."}],"OA_type":"free access","publication_status":"published","oa_version":"Accepted Version","_id":"783","title":"How to elect a leader faster than a tournament","fulldoi":"https://doi.org/10.1145/2767386.2767420","citation":{"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.","ama":"Alistarh D-A, Gelashvili R, Vladu A. How to elect a leader faster than a tournament. In: Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2015:365-374. doi:10.1145/2767386.2767420","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Adrian Vladu. “How to Elect a Leader Faster than a Tournament.” In Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, 365–74. Association for Computing Machinery, 2015. https://doi.org/10.1145/2767386.2767420.","ieee":"D.-A. Alistarh, R. Gelashvili, and A. Vladu, “How to elect a leader faster than a tournament,” in Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, New York, NY, United States, 2015, pp. 365–374.","apa":"Alistarh, D.-A., Gelashvili, R., & Vladu, A. (2015). How to elect a leader faster than a tournament. In Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing (pp. 365–374). New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2767386.2767420","mla":"Alistarh, Dan-Adrian, et al. “How to Elect a Leader Faster than a Tournament.” Proceedings of the 2015 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2015, pp. 365–74, doi:10.1145/2767386.2767420.","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."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"21","month":"07","status":"public","date_created":"2018-12-11T11:48:28Z","publication_identifier":{"isbn":["9781450336178"]},"publist_id":"6875","doi":"10.1145/2767386.2767420","language":[{"iso":"eng"}],"oa":1,"page":"365 - 374","external_id":{"arxiv":["1411.1001"]}}]