[{"author":[{"first_name":"Marco","last_name":"Baity-Jesi","full_name":"Baity-Jesi, Marco"},{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter","last_name":"Goodrich","first_name":"Carl Peter"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"full_name":"Nagel, Sidney R.","last_name":"Nagel","first_name":"Sidney R."},{"full_name":"Sethna, James P.","last_name":"Sethna","first_name":"James P."}],"article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Baity-Jesi, Marco, et al. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer Nature, 2017, pp. 735–48, doi:<a href=\"https://doi.org/10.1007/s10955-016-1703-9\">10.1007/s10955-016-1703-9</a>.","apa":"Baity-Jesi, M., Goodrich, C. P., Liu, A. J., Nagel, S. R., &#38; Sethna, J. P. (2017). Emergent SO(3) symmetry of the frictionless shear jamming transition. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-016-1703-9\">https://doi.org/10.1007/s10955-016-1703-9</a>","ama":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. Emergent SO(3) symmetry of the frictionless shear jamming transition. <i>Journal of Statistical Physics</i>. 2017;167(3-4):735-748. doi:<a href=\"https://doi.org/10.1007/s10955-016-1703-9\">10.1007/s10955-016-1703-9</a>","ieee":"M. Baity-Jesi, C. P. Goodrich, A. J. Liu, S. R. Nagel, and J. P. Sethna, “Emergent SO(3) symmetry of the frictionless shear jamming transition,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer Nature, pp. 735–748, 2017.","ista":"Baity-Jesi M, Goodrich CP, Liu AJ, Nagel SR, Sethna JP. 2017. Emergent SO(3) symmetry of the frictionless shear jamming transition. Journal of Statistical Physics. 167(3–4), 735–748.","short":"M. Baity-Jesi, C.P. Goodrich, A.J. Liu, S.R. Nagel, J.P. Sethna, Journal of Statistical Physics 167 (2017) 735–748.","chicago":"Baity-Jesi, Marco, Carl Peter Goodrich, Andrea J. Liu, Sidney R. Nagel, and James P. Sethna. “Emergent SO(3) Symmetry of the Frictionless Shear Jamming Transition.” <i>Journal of Statistical Physics</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1703-9\">https://doi.org/10.1007/s10955-016-1703-9</a>."},"day":"03","year":"2017","type":"journal_article","date_updated":"2021-01-12T08:15:19Z","oa_version":"None","language":[{"iso":"eng"}],"doi":"10.1007/s10955-016-1703-9","_id":"7756","publication":"Journal of Statistical Physics","title":"Emergent SO(3) symmetry of the frictionless shear jamming transition","publication_status":"published","abstract":[{"text":"We study the shear jamming of athermal frictionless soft spheres, and find that in the thermodynamic limit, a shear-jammed state exists with different elastic properties from the isotropically-jammed state. For example, shear-jammed states can have a non-zero residual shear stress in the thermodynamic limit that arises from long-range stress-stress correlations. As a result, the ratio of the shear and bulk moduli, which in isotropically-jammed systems vanishes as the jamming transition is approached from above, instead approaches a constant. Despite these striking differences, we argue that in a deeper sense, the shear jamming and isotropic jamming transitions actually have the same symmetry, and that the differences can be fully understood by rotating the six-dimensional basis of the elastic modulus tensor.","lang":"eng"}],"page":"735-748","issue":"3-4","volume":167,"date_published":"2017-01-03T00:00:00Z","article_type":"original","publisher":"Springer Nature","publication_identifier":{"issn":["0022-4715","1572-9613"]},"intvolume":"       167","status":"public","date_created":"2020-04-30T11:38:38Z","month":"01"},{"_id":"7757","doi":"10.1073/pnas.1612139114","language":[{"iso":"eng"}],"title":"Designing allostery-inspired response in mechanical networks","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","text":"Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks."}],"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","author":[{"last_name":"Rocks","first_name":"Jason W.","full_name":"Rocks, Jason W."},{"full_name":"Pashine, Nidhi","first_name":"Nidhi","last_name":"Pashine"},{"full_name":"Bischofberger, Irmgard","first_name":"Irmgard","last_name":"Bischofberger"},{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Liu, Andrea J.","last_name":"Liu","first_name":"Andrea J."},{"full_name":"Nagel, Sidney R.","first_name":"Sidney R.","last_name":"Nagel"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(10):2520-2525. doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>","ieee":"J. W. Rocks, N. Pashine, I. Bischofberger, C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Designing allostery-inspired response in mechanical networks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10. Proceedings of the National Academy of Sciences, pp. 2520–2525, 2017.","ista":"Rocks JW, Pashine N, Bischofberger I, Goodrich CP, Liu AJ, Nagel SR. 2017. Designing allostery-inspired response in mechanical networks. Proceedings of the National Academy of Sciences. 114(10), 2520–2525.","chicago":"Rocks, Jason W., Nidhi Pashine, Irmgard Bischofberger, Carl Peter Goodrich, Andrea J. Liu, and Sidney R. Nagel. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>.","short":"J.W. Rocks, N. Pashine, I. Bischofberger, C.P. Goodrich, A.J. Liu, S.R. Nagel, Proceedings of the National Academy of Sciences 114 (2017) 2520–2525.","mla":"Rocks, Jason W., et al. “Designing Allostery-Inspired Response in Mechanical Networks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 10, Proceedings of the National Academy of Sciences, 2017, pp. 2520–25, doi:<a href=\"https://doi.org/10.1073/pnas.1612139114\">10.1073/pnas.1612139114</a>.","apa":"Rocks, J. W., Pashine, N., Bischofberger, I., Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2017). Designing allostery-inspired response in mechanical networks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1612139114\">https://doi.org/10.1073/pnas.1612139114</a>"},"year":"2017","day":"07","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:19Z","publication_identifier":{"issn":["0027-8424","1091-6490"]},"intvolume":"       114","status":"public","month":"03","date_created":"2020-04-30T11:38:53Z","issue":"10","page":"2520-2525","volume":114,"date_published":"2017-03-07T00:00:00Z","publisher":"Proceedings of the National Academy of Sciences","article_type":"original"},{"date_published":"2017-01-10T00:00:00Z","volume":114,"issue":"2","page":"257-262","publisher":"Proceedings of the National Academy of Sciences","article_type":"original","intvolume":"       114","publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"01","date_created":"2020-04-30T11:39:09Z","status":"public","citation":{"ama":"Goodrich CP, Brenner MP. Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(2):257-262. doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>","ieee":"C. P. Goodrich and M. P. Brenner, “Using active colloids as machines to weave and braid on the micrometer scale,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2. Proceedings of the National Academy of Sciences, pp. 257–262, 2017.","ista":"Goodrich CP, Brenner MP. 2017. Using active colloids as machines to weave and braid on the micrometer scale. Proceedings of the National Academy of Sciences. 114(2), 257–262.","short":"C.P. Goodrich, M.P. Brenner, Proceedings of the National Academy of Sciences 114 (2017) 257–262.","chicago":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>.","mla":"Goodrich, Carl Peter, and Michael P. Brenner. “Using Active Colloids as Machines to Weave and Braid on the Micrometer Scale.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 2, Proceedings of the National Academy of Sciences, 2017, pp. 257–62, doi:<a href=\"https://doi.org/10.1073/pnas.1608838114\">10.1073/pnas.1608838114</a>.","apa":"Goodrich, C. P., &#38; Brenner, M. P. (2017). Using active colloids as machines to weave and braid on the micrometer scale. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1608838114\">https://doi.org/10.1073/pnas.1608838114</a>"},"author":[{"last_name":"Goodrich","first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Brenner, Michael P.","last_name":"Brenner","first_name":"Michael P."}],"extern":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T08:15:20Z","year":"2017","day":"10","publication":"Proceedings of the National Academy of Sciences","title":"Using active colloids as machines to weave and braid on the micrometer scale","_id":"7758","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1608838114","abstract":[{"lang":"eng","text":"Controlling motion at the microscopic scale is a fundamental goal in the development of biologically inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the 2D motion of active colloids so that their path has a nontrivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semiflexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that nonequilibrium assembly pathways can be designed using active particles."}],"publication_status":"published"},{"oa":1,"doi":"doi.org/10.1137/1.9781611974782.169","language":[{"iso":"eng"}],"_id":"787","title":"Time-space trade-offs in population protocols","publication_status":"published","abstract":[{"lang":"eng","text":"Population protocols are a popular model of distributed computing, in which randomly-interacting agents with little computational power cooperate to jointly perform computational tasks. Inspired by developments in molecular computation, and in particular DNA computing, recent algorithmic work has focused on the complexity of solving simple yet fundamental tasks in the population model, such as leader election (which requires convergence to a single agent in a special &quot;leader&quot; state), and majority (in which agents must converge to a decision as to which of two possible initial states had higher initial count). Known results point towards an inherent trade-off between the time complexity of such algorithms, and the space complexity, i.e. size of the memory available to each agent. In this paper, we explore this trade-off and provide new upper and lower bounds for majority and leader election. First, we prove a unified lower bound, which relates the space available per node with the time complexity achievable by a protocol: for instance, our result implies that any protocol solving either of these tasks for n agents using O(log log n) states must take (n=polylogn) expected time. This is the first result to characterize time complexity for protocols which employ super-constant number of states per node, and proves that fast, poly-logarithmic running times require protocols to have relatively large space costs. On the positive side, we give algorithms showing that fast, poly-logarithmic convergence time can be achieved using O(log2 n) space per node, in the case of both tasks. Overall, our results highlight a time complexity separation between O(log log n) and (log2 n) state space size for both majority and leader election in population protocols, and introduce new techniques, which should be applicable more broadly."}],"acknowledgement":"Dan  Alistarh  was  supported  by  a  Swiss  National  Science\r\nFoundation Ambizione Fellowship.  James Aspnes was supported  by  the  National  Science  Foundation  under  grants\r\nCCF-1637385 and CCF-1650596.  Rati Gelashvili was supported  by  the  National  Science  Foundation  under  grants\r\nCCF-1217921, CCF-1301926, and IIS-1447786, the Department of Energy under grant ER26116/DE-SC0008923, and\r\nOracle and Intel corporations.\r\nThe  authors  would  like  to  thank  David  Doty,  David\r\nSoloveichik,  and Milan Vojnovic for insightful discussions\r\nand feedback during the development of this work.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"last_name":"Eisenstat","first_name":"David","full_name":"Eisenstat, David"},{"last_name":"Rivest","first_name":"Ronald","full_name":"Rivest, Ronald"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"}],"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1602.08032","open_access":"1"}],"citation":{"ista":"Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. 2017. Time-space trade-offs in population protocols. SODA: Symposium on Discrete Algorithms, 2560–2579.","short":"D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, R. Gelashvili, in:, SIAM, 2017, pp. 2560–2579.","chicago":"Alistarh, Dan-Adrian, James Aspnes, David Eisenstat, Ronald Rivest, and Rati Gelashvili. “Time-Space Trade-Offs in Population Protocols,” 2560–79. SIAM, 2017. <a href=\"https://doi.org/doi.org/10.1137/1.9781611974782.169\">https://doi.org/doi.org/10.1137/1.9781611974782.169</a>.","ama":"Alistarh D-A, Aspnes J, Eisenstat D, Rivest R, Gelashvili R. Time-space trade-offs in population protocols. In: SIAM; 2017:2560-2579. doi:<a href=\"https://doi.org/doi.org/10.1137/1.9781611974782.169\">doi.org/10.1137/1.9781611974782.169</a>","ieee":"D.-A. Alistarh, J. Aspnes, D. Eisenstat, R. Rivest, and R. Gelashvili, “Time-space trade-offs in population protocols,” presented at the SODA: Symposium on Discrete Algorithms, 2017, pp. 2560–2579.","apa":"Alistarh, D.-A., Aspnes, J., Eisenstat, D., Rivest, R., &#38; Gelashvili, R. (2017). Time-space trade-offs in population protocols (pp. 2560–2579). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. <a href=\"https://doi.org/doi.org/10.1137/1.9781611974782.169\">https://doi.org/doi.org/10.1137/1.9781611974782.169</a>","mla":"Alistarh, Dan-Adrian, et al. <i>Time-Space Trade-Offs in Population Protocols</i>. SIAM, 2017, pp. 2560–79, doi:<a href=\"https://doi.org/doi.org/10.1137/1.9781611974782.169\">doi.org/10.1137/1.9781611974782.169</a>."},"day":"01","year":"2017","type":"conference","date_updated":"2023-02-23T13:19:13Z","oa_version":"None","publist_id":"6869","status":"public","date_created":"2018-12-11T11:48:30Z","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"month":"01","page":"2560 - 2579","date_published":"2017-01-01T00:00:00Z","publisher":"SIAM"},{"page":"155 - 171","date_published":"2017-01-01T00:00:00Z","external_id":{"arxiv":["1706.09937"]},"arxiv":1,"scopus_import":"1","alternative_title":["LNCS"],"day":"01","type":"conference","date_updated":"2022-03-18T12:48:02Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","acknowledgement":"D. Alistarh - Supported by an SNF Ambizione Fellowship. A. Kosowski — Supported by Inria project GANG, ANR project DESCARTES, and\r\nNCN grant 2015/17/B/ST6/01897. D. Soloveichik — Supported by NSF grants CCF-1618895 and CCF-1652824.\r\n\r\n","doi":"10.1007/978-3-319-66799-7_11","language":[{"iso":"eng"}],"publisher":"Springer","volume":"10467 LNCS","status":"public","date_created":"2018-12-11T11:48:30Z","month":"01","conference":{"name":"DNA Computing and Molecular Programming"},"publist_id":"6868","year":"2017","extern":"1","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dudek","first_name":"Bartłomiej","full_name":"Dudek, Bartłomiej"},{"full_name":"Kosowski, Adrian","last_name":"Kosowski","first_name":"Adrian"},{"last_name":"Soloveichik","first_name":"David","full_name":"Soloveichik, David"},{"last_name":"Uznański","first_name":"Przemysław","full_name":"Uznański, Przemysław"}],"quality_controlled":"1","citation":{"ieee":"D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, and P. Uznański, “Robust detection in leak-prone population protocols,” presented at the DNA Computing and Molecular Programming, 2017, vol. 10467 LNCS, pp. 155–171.","ama":"Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. Robust detection in leak-prone population protocols. In: Vol 10467 LNCS. Springer; 2017:155-171. doi:<a href=\"https://doi.org/10.1007/978-3-319-66799-7_11\">10.1007/978-3-319-66799-7_11</a>","chicago":"Alistarh, Dan-Adrian, Bartłomiej Dudek, Adrian Kosowski, David Soloveichik, and Przemysław Uznański. “Robust Detection in Leak-Prone Population Protocols,” 10467 LNCS:155–71. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-66799-7_11\">https://doi.org/10.1007/978-3-319-66799-7_11</a>.","short":"D.-A. Alistarh, B. Dudek, A. Kosowski, D. Soloveichik, P. Uznański, in:, Springer, 2017, pp. 155–171.","ista":"Alistarh D-A, Dudek B, Kosowski A, Soloveichik D, Uznański P. 2017. Robust detection in leak-prone population protocols. DNA Computing and Molecular Programming, LNCS, vol. 10467 LNCS, 155–171.","mla":"Alistarh, Dan-Adrian, et al. <i>Robust Detection in Leak-Prone Population Protocols</i>. Vol. 10467 LNCS, Springer, 2017, pp. 155–71, doi:<a href=\"https://doi.org/10.1007/978-3-319-66799-7_11\">10.1007/978-3-319-66799-7_11</a>.","apa":"Alistarh, D.-A., Dudek, B., Kosowski, A., Soloveichik, D., &#38; Uznański, P. (2017). Robust detection in leak-prone population protocols (Vol. 10467 LNCS, pp. 155–171). Presented at the DNA Computing and Molecular Programming, Springer. <a href=\"https://doi.org/10.1007/978-3-319-66799-7_11\">https://doi.org/10.1007/978-3-319-66799-7_11</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1706.09937","open_access":"1"}],"publication_status":"published","abstract":[{"text":"In contrast to electronic computation, chemical computation is noisy and susceptible to a variety of sources of error, which has prevented the construction of robust complex systems. To be effective, chemical algorithms must be designed with an appropriate error model in mind. Here we consider the model of chemical reaction networks that preserve molecular count (population protocols), and ask whether computation can be made robust to a natural model of unintended “leak” reactions. Our definition of leak is motivated by both the particular spurious behavior seen when implementing chemical reaction networks with DNA strand displacement cascades, as well as the unavoidable side reactions in any implementation due to the basic laws of chemistry. We develop a new “Robust Detection” algorithm for the problem of fast (logarithmic time) single molecule detection, and prove that it is robust to this general model of leaks. Besides potential applications in single molecule detection, the error-correction ideas developed here might enable a new class of robust-by-design chemical algorithms. Our analysis is based on a non-standard hybrid argument, combining ideas from discrete analysis of population protocols with classic Markov chain techniques.","lang":"eng"}],"oa":1,"_id":"788","title":"Robust detection in leak-prone population protocols"},{"date_created":"2018-12-11T11:48:30Z","month":"01","conference":{"name":"EuroSys: European Conference on Computer Systems"},"status":"public","publist_id":"6867","publisher":"ACM","date_published":"2017-01-01T00:00:00Z","page":"483 - 498","acknowledgement":"William Leiserson, Alexander Matveev, and Nir Shavit were supported by the NSF under grants IIS-1447786 and CCF-1563880, and Dan Alistarh was supported by a Swiss National Fund Ambizione Fellowship.","publication_status":"published","abstract":[{"text":"The problem of efficient concurrent memory reclamation in unmanaged languages such as C or C++ is one of the major challenges facing the parallelization of billions of lines of legacy code. Garbage collectors for C/C++ can be inefficient; thus, programmers are often forced to use finely-crafted concurrent memory reclamation techniques. These techniques can provide good performance, but require considerable programming effort to deploy, and have strict requirements, allowing the programmer very little room for error. In this work, we present Forkscan, a new conservative concurrent memory reclamation scheme which is fully automatic and surprisingly scalable. Forkscan's semantics place it between automatic garbage collectors (it requires the programmer to explicitly retire nodes before they can be reclaimed), and concurrent memory reclamation techniques (as it does not assume that nodes are completely unlinked from the data structure for correctness). Forkscan's implementation exploits these new semantics for efficiency: we leverage parallelism and optimized implementations of signaling and copy-on-write in modern operating systems to efficiently obtain and process consistent snapshots of memory that can be scanned concurrently with the normal program operation. Empirical evaluation on a range of classical concurrent data structure microbenchmarks shows that Forkscan can preserve the scalability of the original code, while maintaining an order of magnitude lower latency than automatic garbage collection, and demonstrating competitive performance with finely crafted memory reclamation techniques.","lang":"eng"}],"title":"Forkscan: Conservative memory reclamation for modern operating systems","language":[{"iso":"eng"}],"doi":"10.1145/3064176.3064214","_id":"789","type":"conference","date_updated":"2023-02-23T13:19:44Z","oa_version":"None","day":"01","year":"2017","citation":{"mla":"Alistarh, Dan-Adrian, et al. <i>Forkscan: Conservative Memory Reclamation for Modern Operating Systems</i>. ACM, 2017, pp. 483–98, doi:<a href=\"https://doi.org/10.1145/3064176.3064214\">10.1145/3064176.3064214</a>.","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., &#38; Shavit, N. (2017). Forkscan: Conservative memory reclamation for modern operating systems (pp. 483–498). Presented at the EuroSys: European Conference on Computer Systems, ACM. <a href=\"https://doi.org/10.1145/3064176.3064214\">https://doi.org/10.1145/3064176.3064214</a>","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, in:, ACM, 2017, pp. 483–498.","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “Forkscan: Conservative Memory Reclamation for Modern Operating Systems,” 483–98. ACM, 2017. <a href=\"https://doi.org/10.1145/3064176.3064214\">https://doi.org/10.1145/3064176.3064214</a>.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2017. Forkscan: Conservative memory reclamation for modern operating systems. EuroSys: European Conference on Computer Systems, 483–498.","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. Forkscan: Conservative memory reclamation for modern operating systems. In: ACM; 2017:483-498. doi:<a href=\"https://doi.org/10.1145/3064176.3064214\">10.1145/3064176.3064214</a>","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “Forkscan: Conservative memory reclamation for modern operating systems,” presented at the EuroSys: European Conference on Computer Systems, 2017, pp. 483–498."},"article_processing_charge":"No","extern":"1","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Leiserson, William","last_name":"Leiserson","first_name":"William"},{"last_name":"Matveev","first_name":"Alexander","full_name":"Matveev, Alexander"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"conference":{"name":"FCCM: Field-Programmable Custom Computing Machines"},"month":"06","date_created":"2018-12-11T11:48:31Z","status":"public","publist_id":"6865","publisher":"IEEE","date_published":"2017-06-30T00:00:00Z","page":"160 - 167","abstract":[{"lang":"eng","text":"Stochastic gradient descent (SGD) is a commonly used algorithm for training linear machine learning models. Based on vector algebra, it benefits from the inherent parallelism available in an FPGA. In this paper, we first present a single-precision floating-point SGD implementation on an FPGA that provides similar performance as a 10-core CPU. We then adapt the design to make it capable of processing low-precision data. The low-precision data is obtained from a novel compression scheme - called stochastic quantization, specifically designed for machine learning applications. We test both full-precision and low-precision designs on various regression and classification data sets. We achieve up to an order of magnitude training speedup when using low-precision data compared to a full-precision SGD on the same FPGA and a state-of-the-art multi-core solution, while maintaining the quality of training. We open source the designs presented in this paper."}],"publication_status":"published","title":"FPGA-accelerated dense linear machine learning: A precision-convergence trade-off","_id":"790","language":[{"iso":"eng"}],"doi":"10.1109/FCCM.2017.39","oa_version":"None","date_updated":"2023-02-23T13:19:52Z","type":"conference","year":"2017","day":"30","citation":{"ista":"Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. 2017. FPGA-accelerated dense linear machine learning: A precision-convergence trade-off. FCCM: Field-Programmable Custom Computing Machines, 160–167.","short":"K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, C. Zhang, in:, IEEE, 2017, pp. 160–167.","chicago":"Kara, Kaan, Dan-Adrian Alistarh, Gustavo Alonso, Onur Mutlu, and Ce Zhang. “FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off,” 160–67. IEEE, 2017. <a href=\"https://doi.org/10.1109/FCCM.2017.39\">https://doi.org/10.1109/FCCM.2017.39</a>.","ieee":"K. Kara, D.-A. Alistarh, G. Alonso, O. Mutlu, and C. Zhang, “FPGA-accelerated dense linear machine learning: A precision-convergence trade-off,” presented at the FCCM: Field-Programmable Custom Computing Machines, 2017, pp. 160–167.","ama":"Kara K, Alistarh D-A, Alonso G, Mutlu O, Zhang C. FPGA-accelerated dense linear machine learning: A precision-convergence trade-off. In: IEEE; 2017:160-167. doi:<a href=\"https://doi.org/10.1109/FCCM.2017.39\">10.1109/FCCM.2017.39</a>","apa":"Kara, K., Alistarh, D.-A., Alonso, G., Mutlu, O., &#38; Zhang, C. (2017). FPGA-accelerated dense linear machine learning: A precision-convergence trade-off (pp. 160–167). Presented at the FCCM: Field-Programmable Custom Computing Machines, IEEE. <a href=\"https://doi.org/10.1109/FCCM.2017.39\">https://doi.org/10.1109/FCCM.2017.39</a>","mla":"Kara, Kaan, et al. <i>FPGA-Accelerated Dense Linear Machine Learning: A Precision-Convergence Trade-Off</i>. IEEE, 2017, pp. 160–67, doi:<a href=\"https://doi.org/10.1109/FCCM.2017.39\">10.1109/FCCM.2017.39</a>."},"extern":"1","article_processing_charge":"No","author":[{"first_name":"Kaan","last_name":"Kara","full_name":"Kara, Kaan"},{"last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Alonso, Gustavo","first_name":"Gustavo","last_name":"Alonso"},{"last_name":"Mutlu","first_name":"Onur","full_name":"Mutlu, Onur"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"26","oa_version":"Submitted Version","date_updated":"2023-09-27T12:17:59Z","type":"conference","department":[{"_id":"DaAl"}],"doi":"10.1145/3087801.3087810","language":[{"iso":"eng"}],"page":"283 - 292","external_id":{"isi":["000462995000035"]},"date_published":"2017-07-26T00:00:00Z","scopus_import":"1","publication_identifier":{"isbn":["978-145034992-5"]},"author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Justin","last_name":"Kopinsky","full_name":"Kopinsky, Justin"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"},{"first_name":"Giorgi","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.04178","open_access":"1"}],"citation":{"short":"D.-A. Alistarh, J. Kopinsky, J. Li, G. Nadiradze, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, ACM, 2017, pp. 283–292.","chicago":"Alistarh, Dan-Adrian, Justin Kopinsky, Jerry Li, and Giorgi Nadiradze. “The Power of Choice in Priority Scheduling.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Part F129314:283–92. ACM, 2017. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>.","ista":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. 2017. The power of choice in priority scheduling. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing vol. Part F129314, 283–292.","ama":"Alistarh D-A, Kopinsky J, Li J, Nadiradze G. The power of choice in priority scheduling. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Vol Part F129314. ACM; 2017:283-292. doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>","ieee":"D.-A. Alistarh, J. Kopinsky, J. Li, and G. Nadiradze, “The power of choice in priority scheduling,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Washington, WA, USA, 2017, vol. Part F129314, pp. 283–292.","mla":"Alistarh, Dan-Adrian, et al. “The Power of Choice in Priority Scheduling.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, vol. Part F129314, ACM, 2017, pp. 283–92, doi:<a href=\"https://doi.org/10.1145/3087801.3087810\">10.1145/3087801.3087810</a>.","apa":"Alistarh, D.-A., Kopinsky, J., Li, J., &#38; Nadiradze, G. (2017). The power of choice in priority scheduling. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (Vol. Part F129314, pp. 283–292). Washington, WA, USA: ACM. <a href=\"https://doi.org/10.1145/3087801.3087810\">https://doi.org/10.1145/3087801.3087810</a>"},"year":"2017","_id":"791","oa":1,"title":"The power of choice in priority scheduling","publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","abstract":[{"text":"Consider the following random process: we are given n queues, into which elements of increasing labels are inserted uniformly at random. To remove an element, we pick two queues at random, and remove the element of lower label (higher priority) among the two. The cost of a removal is the rank of the label removed, among labels still present in any of the queues, that is, the distance from the optimal choice at each step. Variants of this strategy are prevalent in state-of-the-art concurrent priority queue implementations. Nonetheless, it is not known whether such implementations provide any rank guarantees, even in a sequential model. We answer this question, showing that this strategy provides surprisingly strong guarantees: Although the single-choice process, where we always insert and remove from a single randomly chosen queue, has degrading cost, going to infinity as we increase the number of steps, in the two choice process, the expected rank of a removed element is O(n) while the expected worst-case cost is O(n log n). These bounds are tight, and hold irrespective of the number of steps for which we run the process. The argument is based on a new technical connection between &quot;heavily loaded&quot; balls-into-bins processes and priority scheduling. Our analytic results inspire a new concurrent priority queue implementation, which improves upon the state of the art in terms of practical performance.","lang":"eng"}],"publication_status":"published","volume":"Part F129314","publisher":"ACM","isi":1,"publist_id":"6864","status":"public","month":"07","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2017-07-27","location":"Washington, WA, USA","start_date":"2017-07-25"},"date_created":"2018-12-11T11:48:31Z"},{"date_published":"2017-12-25T00:00:00Z","external_id":{"isi":["000414641700001"]},"page":"274 - 301","publication_identifier":{"issn":["00221120"]},"scopus_import":"1","date_updated":"2023-09-27T12:17:35Z","type":"journal_article","oa_version":"Submitted Version","day":"25","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1017/jfm.2017.699","language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"publisher":"Cambridge University Press","volume":833,"date_created":"2018-12-11T11:48:32Z","month":"12","status":"public","intvolume":"       833","publist_id":"6862","isi":1,"year":"2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.03720"}],"citation":{"ista":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. 2017. Relative periodic orbits form the backbone of turbulent pipe flow. Journal of Fluid Mechanics. 833, 274–301.","short":"N.B. Budanur, K. Short, M. Farazmand, A. Willis, P. Cvitanović, Journal of Fluid Mechanics 833 (2017) 274–301.","chicago":"Budanur, Nazmi B, Kimberly Short, Mohammad Farazmand, Ashley Willis, and Predrag Cvitanović. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>.","ieee":"N. B. Budanur, K. Short, M. Farazmand, A. Willis, and P. Cvitanović, “Relative periodic orbits form the backbone of turbulent pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 833. Cambridge University Press, pp. 274–301, 2017.","ama":"Budanur NB, Short K, Farazmand M, Willis A, Cvitanović P. Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;833:274-301. doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>","apa":"Budanur, N. B., Short, K., Farazmand, M., Willis, A., &#38; Cvitanović, P. (2017). Relative periodic orbits form the backbone of turbulent pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.699\">https://doi.org/10.1017/jfm.2017.699</a>","mla":"Budanur, Nazmi B., et al. “Relative Periodic Orbits Form the Backbone of Turbulent Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 833, Cambridge University Press, 2017, pp. 274–301, doi:<a href=\"https://doi.org/10.1017/jfm.2017.699\">10.1017/jfm.2017.699</a>."},"author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B"},{"first_name":"Kimberly","last_name":"Short","full_name":"Short, Kimberly"},{"full_name":"Farazmand, Mohammad","last_name":"Farazmand","first_name":"Mohammad"},{"first_name":"Ashley","last_name":"Willis","full_name":"Willis, Ashley"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"quality_controlled":"1","project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"publication_status":"published","abstract":[{"lang":"eng","text":"The chaotic dynamics of low-dimensional systems, such as Lorenz or Rössler flows, is guided by the infinity of periodic orbits embedded in their strange attractors. Whether this is also the case for the infinite-dimensional dynamics of Navier–Stokes equations has long been speculated, and is a topic of ongoing study. Periodic and relative periodic solutions have been shown to be involved in transitions to turbulence. Their relevance to turbulent dynamics – specifically, whether periodic orbits play the same role in high-dimensional nonlinear systems like the Navier–Stokes equations as they do in lower-dimensional systems – is the focus of the present investigation. We perform here a detailed study of pipe flow relative periodic orbits with energies and mean dissipations close to turbulent values. We outline several approaches to reduction of the translational symmetry of the system. We study pipe flow in a minimal computational cell at   Re=2500, and report a library of invariant solutions found with the aid of the method of slices. Detailed study of the unstable manifolds of a sample of these solutions is consistent with the picture that relative periodic orbits are embedded in the chaotic saddle and that they guide the turbulent dynamics."}],"title":"Relative periodic orbits form the backbone of turbulent pipe flow","publication":"Journal of Fluid Mechanics","oa":1,"_id":"792"},{"publisher":"Elsevier","volume":66,"month":"01","date_created":"2018-12-11T11:48:32Z","status":"public","intvolume":"        66","isi":1,"publist_id":"6861","year":"2017","citation":{"ista":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. 2017. On the existence of ordinary triangles. Computational Geometry: Theory and Applications. 66, 28–31.","short":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, M. Szedlák, Computational Geometry: Theory and Applications 66 (2017) 28–31.","chicago":"Fulek, Radoslav, Hossein Mojarrad, Márton Naszódi, József Solymosi, Sebastian Stich, and May Szedlák. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>.","ama":"Fulek R, Mojarrad H, Naszódi M, Solymosi J, Stich S, Szedlák M. On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. 2017;66:28-31. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>","ieee":"R. Fulek, H. Mojarrad, M. Naszódi, J. Solymosi, S. Stich, and M. Szedlák, “On the existence of ordinary triangles,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 28–31, 2017.","apa":"Fulek, R., Mojarrad, H., Naszódi, M., Solymosi, J., Stich, S., &#38; Szedlák, M. (2017). On the existence of ordinary triangles. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">https://doi.org/10.1016/j.comgeo.2017.07.002</a>","mla":"Fulek, Radoslav, et al. “On the Existence of Ordinary Triangles.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 28–31, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.07.002\">10.1016/j.comgeo.2017.07.002</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1701.08183","open_access":"1"}],"author":[{"last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Mojarrad, Hossein","first_name":"Hossein","last_name":"Mojarrad"},{"full_name":"Naszódi, Márton","first_name":"Márton","last_name":"Naszódi"},{"first_name":"József","last_name":"Solymosi","full_name":"Solymosi, József"},{"full_name":"Stich, Sebastian","first_name":"Sebastian","last_name":"Stich"},{"full_name":"Szedlák, May","first_name":"May","last_name":"Szedlák"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"text":"Let P be a finite point set in the plane. A cordinary triangle in P is a subset of P consisting of three non-collinear points such that each of the three lines determined by the three points contains at most c points of P . Motivated by a question of Erdös, and answering a question of de Zeeuw, we prove that there exists a constant c &gt; 0such that P contains a c-ordinary triangle, provided that P is not contained in the union of two lines. Furthermore, the number of c-ordinary triangles in P is Ω(| P |). ","lang":"eng"}],"publication_status":"published","publication":"Computational Geometry: Theory and Applications","title":"On the existence of ordinary triangles","_id":"793","oa":1,"external_id":{"isi":["000412039700003"]},"date_published":"2017-01-01T00:00:00Z","page":"28 - 31","publication_identifier":{"issn":["09257721"]},"oa_version":"Submitted Version","date_updated":"2023-09-27T12:15:16Z","type":"journal_article","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","ec_funded":1,"department":[{"_id":"UlWa"}],"doi":"10.1016/j.comgeo.2017.07.002","language":[{"iso":"eng"}]},{"volume":66,"publisher":"Elsevier","isi":1,"publist_id":"6860","intvolume":"        66","status":"public","month":"12","date_created":"2018-12-11T11:48:32Z","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.01346"}],"citation":{"mla":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>, vol. 66, Elsevier, 2017, pp. 1–13, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>.","apa":"Fulek, R. (2017). C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. <i>Computational Geometry: Theory and Applications</i>. 2017;66:1-13. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">10.1016/j.comgeo.2017.06.016</a>","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” <i>Computational Geometry: Theory and Applications</i>, vol. 66. Elsevier, pp. 1–13, 2017.","ista":"Fulek R. 2017. C-planarity of embedded cyclic c-graphs. Computational Geometry: Theory and Applications. 66, 1–13.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.016\">https://doi.org/10.1016/j.comgeo.2017.06.016</a>.","short":"R. Fulek, Computational Geometry: Theory and Applications 66 (2017) 1–13."},"year":"2017","_id":"794","related_material":{"record":[{"id":"1165","status":"public","relation":"earlier_version"}]},"oa":1,"publication":"Computational Geometry: Theory and Applications","title":"C-planarity of embedded cyclic c-graphs","abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"publication_status":"published","page":"1 - 13","external_id":{"isi":["000412039700001"]},"date_published":"2017-12-01T00:00:00Z","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","oa_version":"Preprint","type":"journal_article","date_updated":"2023-09-27T12:14:49Z","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2017.06.016","acknowledgement":"I would like to thank Jan Kynčl, Dömötör Pálvölgyi and anonymous referees for many comments and suggestions that helped to improve the presentation of the result."},{"publication_identifier":{"issn":["10778926"]},"scopus_import":"1","date_published":"2017-07-28T00:00:00Z","file":[{"date_updated":"2020-07-14T12:48:06Z","file_id":"5853","file_name":"2017_ElectrCombi_Fulek.pdf","checksum":"ef320cff0f062051e858f929be6a3581","access_level":"open_access","relation":"main_file","date_created":"2019-01-18T14:04:08Z","content_type":"application/pdf","creator":"dernst","file_size":236944}],"doi":"10.37236/6663","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"UlWa"}],"ec_funded":1,"day":"28","date_updated":"2022-03-18T12:58:53Z","type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","status":"public","article_number":"P3.18","date_created":"2018-12-11T11:48:32Z","month":"07","publist_id":"6859","intvolume":"        24","publisher":"International Press","article_type":"original","file_date_updated":"2020-07-14T12:48:06Z","issue":"3","volume":24,"publication_status":"published","abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"ddc":["000"],"oa":1,"_id":"795","title":"Unified Hanani Tutte theorem","publication":"Electronic Journal of Combinatorics","year":"2017","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"quality_controlled":"1","citation":{"apa":"Fulek, R., Kynčl, J., &#38; Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. International Press. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3, P3.18, International Press, 2017, doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>.","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” <i>Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, 2017.","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. <i>Electronic Journal of Combinatorics</i>. 2017;24(3). doi:<a href=\"https://doi.org/10.37236/6663\">10.37236/6663</a>","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” <i>Electronic Journal of Combinatorics</i>. International Press, 2017. <a href=\"https://doi.org/10.37236/6663\">https://doi.org/10.37236/6663</a>.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017)."}},{"oa":1,"_id":"796","title":"Al transmon qubits on silicon on insulator for quantum device integration","publication":"Applied Physics Letters","publication_status":"published","abstract":[{"lang":"eng","text":"We present the fabrication and characterization of an aluminum transmon qubit on a silicon-on-insulator substrate. Key to the qubit fabrication is the use of an anhydrous hydrofluoric vapor process which selectively removes the lossy silicon oxide buried underneath the silicon device layer. For a 5.6 GHz qubit measured dispersively by a 7.1 GHz resonator, we find T1 = 3.5 μs and T∗2 = 2.2 μs. This process in principle permits the co-fabrication of silicon photonic and mechanical elements, providing a route towards chip-scale integration of electro-opto-mechanical transducers for quantum networking of superconducting microwave quantum circuits. The additional processing steps are compatible with established fabrication techniques for aluminum transmon qubits on silicon."}],"author":[{"last_name":"Keller","first_name":"Andrew J","full_name":"Keller, Andrew J"},{"full_name":"Dieterle, Paul","last_name":"Dieterle","first_name":"Paul"},{"first_name":"Michael","last_name":"Fang","full_name":"Fang, Michael"},{"full_name":"Berger, Brett","first_name":"Brett","last_name":"Berger"},{"last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"}],"quality_controlled":"1","citation":{"ieee":"A. J. Keller, P. Dieterle, M. Fang, B. Berger, J. M. Fink, and O. Painter, “Al transmon qubits on silicon on insulator for quantum device integration,” <i>Applied Physics Letters</i>, vol. 111, no. 4. American Institute of Physics, 2017.","ama":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. 2017;111(4). doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>","ista":"Keller AJ, Dieterle P, Fang M, Berger B, Fink JM, Painter O. 2017. Al transmon qubits on silicon on insulator for quantum device integration. Applied Physics Letters. 111(4), 042603.","chicago":"Keller, Andrew J, Paul Dieterle, Michael Fang, Brett Berger, Johannes M Fink, and Oskar Painter. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>.","short":"A.J. Keller, P. Dieterle, M. Fang, B. Berger, J.M. Fink, O. Painter, Applied Physics Letters 111 (2017).","mla":"Keller, Andrew J., et al. “Al Transmon Qubits on Silicon on Insulator for Quantum Device Integration.” <i>Applied Physics Letters</i>, vol. 111, no. 4, 042603, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1063/1.4994661\">10.1063/1.4994661</a>.","apa":"Keller, A. J., Dieterle, P., Fang, M., Berger, B., Fink, J. M., &#38; Painter, O. (2017). Al transmon qubits on silicon on insulator for quantum device integration. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4994661\">https://doi.org/10.1063/1.4994661</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1703.10195","open_access":"1"}],"year":"2017","publist_id":"6857","isi":1,"intvolume":"       111","status":"public","article_number":"042603","date_created":"2018-12-11T11:48:33Z","month":"07","volume":111,"issue":"4","publisher":"American Institute of Physics","language":[{"iso":"eng"}],"doi":"10.1063/1.4994661","department":[{"_id":"JoFi"}],"acknowledgement":"This work was supported by the AFOSR MURI Quantum Photonic Matter (Grant No. 16RT0696), the AFOSR MURI Wiring Quantum Networks with Mechanical Transducers (Grant No. FA9550-15-1-0015), the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center (Grant No. PHY-1125565) with the support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.J.K. acknowledges the IQIM Postdoctoral Fellowship.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","date_updated":"2023-09-27T12:13:36Z","type":"journal_article","oa_version":"Submitted Version","publication_identifier":{"issn":["00036951"]},"scopus_import":"1","date_published":"2017-07-01T00:00:00Z","external_id":{"isi":["000406779700031"]}},{"day":"01","year":"2017","date_updated":"2022-03-24T09:16:20Z","type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink"}],"citation":{"apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. <i>Physik in Unserer Zeit</i>. Wiley. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” <i>Physik in unserer Zeit</i>, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","ama":"Fink JM. Photonenblockade aufgelöst. <i>Physik in unserer Zeit</i>. 2017;48(3):111-113. doi:<a href=\"https://doi.org/10.1002/piuz.201770305\">10.1002/piuz.201770305</a>","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” <i>Physik in Unserer Zeit</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/piuz.201770305\">https://doi.org/10.1002/piuz.201770305</a>.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113."},"publication_status":"published","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"doi":"10.1002/piuz.201770305","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"_id":"797","title":"Photonenblockade aufgelöst","publication":"Physik in unserer Zeit","publisher":"Wiley","article_type":"original","volume":48,"issue":"3","page":"111 - 113","date_published":"2017-05-01T00:00:00Z","status":"public","date_created":"2018-12-11T11:48:33Z","month":"05","publist_id":"6856","intvolume":"        48"},{"_id":"798","oa":1,"ddc":["539"],"publication":"Nature Communications","title":"Mechanical on chip microwave circulator","abstract":[{"text":"Nonreciprocal circuit elements form an integral part of modern measurement and communication systems. Mathematically they require breaking of time-reversal symmetry, typically achieved using magnetic materials and more recently using the quantum Hall effect, parametric permittivity modulation or Josephson nonlinearities. Here we demonstrate an on-chip magnetic-free circulator based on reservoir-engineered electromechanic interactions. Directional circulation is achieved with controlled phase-sensitive interference of six distinct electro-mechanical signal conversion paths. The presented circulator is compact, its silicon-on-insulator platform is compatible with both superconducting qubits and silicon photonics, and its noise performance is close to the quantum limit. With a high dynamic range, a tunable bandwidth of up to 30 MHz and an in situ reconfigurability as beam splitter or wavelength converter, it could pave the way for superconducting qubit processors with multiplexed on-chip signal processing and readout.","lang":"eng"}],"publication_status":"published","project":[{"name":"Hybrid Optomechanical Technologies","grant_number":"732894","call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"author":[{"first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378"},{"orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","last_name":"Peruzzo"},{"full_name":"Kalaee, Mahmoud","last_name":"Kalaee","first_name":"Mahmoud"},{"last_name":"Dieterle","first_name":"Paul","full_name":"Dieterle, Paul"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"}],"quality_controlled":"1","citation":{"ista":"Barzanjeh S, Wulf M, Peruzzo M, Kalaee M, Dieterle P, Painter O, Fink JM. 2017. Mechanical on chip microwave circulator. Nature Communications. 8(1), 1304.","short":"S. Barzanjeh, M. Wulf, M. Peruzzo, M. Kalaee, P. Dieterle, O. Painter, J.M. Fink, Nature Communications 8 (2017).","chicago":"Barzanjeh, Shabir, Matthias Wulf, Matilda Peruzzo, Mahmoud Kalaee, Paul Dieterle, Oskar Painter, and Johannes M Fink. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>.","ama":"Barzanjeh S, Wulf M, Peruzzo M, et al. Mechanical on chip microwave circulator. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>","ieee":"S. Barzanjeh <i>et al.</i>, “Mechanical on chip microwave circulator,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Barzanjeh, S., Wulf, M., Peruzzo, M., Kalaee, M., Dieterle, P., Painter, O., &#38; Fink, J. M. (2017). Mechanical on chip microwave circulator. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01304-x\">https://doi.org/10.1038/s41467-017-01304-x</a>","mla":"Barzanjeh, Shabir, et al. “Mechanical on Chip Microwave Circulator.” <i>Nature Communications</i>, vol. 8, no. 1, 1304, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01304-x\">10.1038/s41467-017-01304-x</a>."},"year":"2017","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"publist_id":"6855","intvolume":"         8","status":"public","article_number":"1304","month":"10","date_created":"2018-12-11T11:48:33Z","pubrep_id":"867","issue":"1","volume":8,"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:48:06Z","has_accepted_license":"1","department":[{"_id":"JoFi"}],"doi":"10.1038/s41467-017-01304-x","license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"16","oa_version":"Published Version","date_updated":"2023-09-27T12:11:28Z","type":"journal_article","scopus_import":"1","publication_identifier":{"issn":["20411723"]},"file":[{"creator":"system","content_type":"application/pdf","file_size":1467696,"date_created":"2018-12-12T10:15:25Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-867-v1+1_s41467-017-01304-x.pdf","checksum":"b68dafa71d1834c23b742cd9987a3d5f","date_updated":"2020-07-14T12:48:06Z","file_id":"5145"}],"external_id":{"isi":["000412999700021"]},"date_published":"2017-10-16T00:00:00Z"},{"has_accepted_license":"1","doi":"10.1007/978-3-319-50754-5_2","language":[{"iso":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","date_updated":"2021-01-12T08:16:19Z","type":"book_chapter","day":"26","alternative_title":["SpringerBriefs in Molecular Science"],"publication_identifier":{"isbn":["9783319507538","9783319507545"],"issn":["2191-5407","2191-5415"]},"file":[{"checksum":"4182aeee32c9263a626a7e522f1934f5","file_name":"Final_EPNOE.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:06Z","file_id":"8048","file_size":3339826,"content_type":"application/pdf","creator":"sfreunbe","relation":"main_file","date_created":"2020-06-29T14:13:44Z"}],"date_published":"2017-03-26T00:00:00Z","page":"15-53","title":"Polysaccharides in supercapacitors","publication":"Polysaccharide Based Supercapacitors","_id":"7980","oa":1,"ddc":["540","541"],"abstract":[{"lang":"eng","text":"In this part, the use of polysaccharides, either directly through composite approaches, or by carbonization will be described. In many cases, materials are obtained which are competitive in terms of capacitance and cycle lifetime. In this part, the use of polysaccharides, either directly through composite approaches, or by carbonization will be described. In many cases, materials are obtained which are competitive in terms of capacitance and cycle lifetime. The following part will focus mainly on cellulosic composites with conductive polymers since cellulose is most abundant and therefore has attracted much more research interest in this field whereas in the second part also other polysaccharides, such as chitin, xylans, alginates, pectins, dextrans and caragenaans have been used in carbonization experiments."}],"publication_status":"published","citation":{"apa":"Yee Liew, S., Thielemans, W., Freunberger, S. A., &#38; Spirk, S. (2017). Polysaccharides in supercapacitors. In S. Yee Liew, W. Thielemans, S. A. Freunberger, &#38; S. Spirk (Eds.), <i>Polysaccharide Based Supercapacitors</i> (pp. 15–53). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-50754-5_2\">https://doi.org/10.1007/978-3-319-50754-5_2</a>","mla":"Yee Liew, Soon, et al. “Polysaccharides in Supercapacitors.” <i>Polysaccharide Based Supercapacitors</i>, edited by Soon Yee Liew et al., Springer Nature, 2017, pp. 15–53, doi:<a href=\"https://doi.org/10.1007/978-3-319-50754-5_2\">10.1007/978-3-319-50754-5_2</a>.","ista":"Yee Liew S, Thielemans W, Freunberger SA, Spirk S. 2017.Polysaccharides in supercapacitors. In: Polysaccharide Based Supercapacitors. SpringerBriefs in Molecular Science, , 15–53.","short":"S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk, in:, S. Yee Liew, W. Thielemans, S.A. Freunberger, S. Spirk (Eds.), Polysaccharide Based Supercapacitors, Springer Nature, 2017, pp. 15–53.","chicago":"Yee Liew, Soon, Wim Thielemans, Stefan Alexander Freunberger, and Stefan Spirk. “Polysaccharides in Supercapacitors.” In <i>Polysaccharide Based Supercapacitors</i>, edited by Soon Yee Liew, Wim Thielemans, Stefan Alexander Freunberger, and Stefan Spirk, 15–53. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-50754-5_2\">https://doi.org/10.1007/978-3-319-50754-5_2</a>.","ieee":"S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, “Polysaccharides in supercapacitors,” in <i>Polysaccharide Based Supercapacitors</i>, S. Yee Liew, W. Thielemans, S. A. Freunberger, and S. Spirk, Eds. Springer Nature, 2017, pp. 15–53.","ama":"Yee Liew S, Thielemans W, Freunberger SA, Spirk S. Polysaccharides in supercapacitors. In: Yee Liew S, Thielemans W, Freunberger SA, Spirk S, eds. <i>Polysaccharide Based Supercapacitors</i>. Springer Nature; 2017:15-53. doi:<a href=\"https://doi.org/10.1007/978-3-319-50754-5_2\">10.1007/978-3-319-50754-5_2</a>"},"extern":"1","author":[{"last_name":"Yee Liew","first_name":"Soon","full_name":"Yee Liew, Soon"},{"full_name":"Thielemans, Wim","last_name":"Thielemans","first_name":"Wim"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"full_name":"Spirk, Stefan","last_name":"Spirk","first_name":"Stefan"}],"quality_controlled":"1","year":"2017","month":"03","date_created":"2020-06-19T08:11:08Z","status":"public","file_date_updated":"2020-07-14T12:48:06Z","editor":[{"first_name":"Soon","last_name":"Yee Liew","full_name":"Yee Liew, Soon"},{"full_name":"Thielemans, Wim","first_name":"Wim","last_name":"Thielemans"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"},{"full_name":"Spirk, Stefan","first_name":"Stefan","last_name":"Spirk"}],"publisher":"Springer Nature"},{"publication_identifier":{"issn":["0044-8249"]},"page":"15934-15938","file":[{"file_id":"7987","date_updated":"2020-07-14T12:48:06Z","access_level":"open_access","file_name":"2017_AngChemieDT_Schafzahl.pdf","checksum":"38f2c2383bc9573f6770c1dba72d7a9a","date_created":"2020-06-19T11:39:09Z","relation":"main_file","file_size":988125,"content_type":"application/pdf","creator":"dernst"}],"date_published":"2017-12-04T00:00:00Z","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"doi":"10.1002/ange.201709351","day":"04","oa_version":"Published Version","date_updated":"2021-01-12T08:16:20Z","type":"journal_article","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","month":"12","date_created":"2020-06-19T08:22:06Z","intvolume":"       129","publisher":"Wiley","article_type":"original","file_date_updated":"2020-07-14T12:48:06Z","volume":129,"issue":"49","abstract":[{"lang":"ger","text":"Aprotische Natrium‐O2‐Batterien basieren auf der reversiblen Bildung und Auflösung von Natriumsuperoxid (NaO2) während des Zellbetriebs. Nebenreaktionen des Elektrolyten und der Elektrode mit dem stark nukleophilen und basischen NaO2 führen zu mangelhafter Zyklenstabilität. Seine Reaktivität allein kann die Nebenreaktionen und schlechte Reversibilität jedoch nicht schlüssig erklären. Hier wird gezeigt, dass Singulett‐Sauerstoff (1O2) in allen Phasen des Betriebs entsteht und eine Hauptursache für Nebenreaktionen ist. 1O2 wurde in situ und ex situ mit einem 1O2‐Fänger detektiert, der schnell und selektiv ein Addukt mit 1O2 bildet. Mechanistisch betrachtet entsteht 1O2 entweder durch protonenunterstützte Disproportionierung von Superoxid während des Entladens, Lagerns und Ladens unter ca. 3.3 V oder durch direkte elektrochemische 1O2‐Entwicklung über ca. 3.3 V. Spuren von Wasser ermöglichen hohe Kapazitäten, beschleunigen aber auch Nebenreaktionen. Daher muss das hochreaktive 1O2 unbedingt kontrolliert werden, um die Zelle reversibel zu betreiben."}],"publication_status":"published","_id":"7981","ddc":["540"],"oa":1,"publication":"Angewandte Chemie","title":"Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie","year":"2017","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"extern":"1","quality_controlled":"1","author":[{"full_name":"Schafzahl, Lukas","first_name":"Lukas","last_name":"Schafzahl"},{"last_name":"Mahne","first_name":"Nika","full_name":"Mahne, Nika"},{"last_name":"Schafzahl","first_name":"Bettina","full_name":"Schafzahl, Bettina"},{"last_name":"Wilkening","first_name":"Martin","full_name":"Wilkening, Martin"},{"full_name":"Slugovc, Christian","first_name":"Christian","last_name":"Slugovc"},{"full_name":"Borisov, Sergey M.","first_name":"Sergey M.","last_name":"Borisov"},{"last_name":"Freunberger","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"}],"citation":{"ieee":"L. Schafzahl <i>et al.</i>, “Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie,” <i>Angewandte Chemie</i>, vol. 129, no. 49. Wiley, pp. 15934–15938, 2017.","ama":"Schafzahl L, Mahne N, Schafzahl B, et al. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. <i>Angewandte Chemie</i>. 2017;129(49):15934-15938. doi:<a href=\"https://doi.org/10.1002/ange.201709351\">10.1002/ange.201709351</a>","short":"L. Schafzahl, N. Mahne, B. Schafzahl, M. Wilkening, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie 129 (2017) 15934–15938.","chicago":"Schafzahl, Lukas, Nika Mahne, Bettina Schafzahl, Martin Wilkening, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.” <i>Angewandte Chemie</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/ange.201709351\">https://doi.org/10.1002/ange.201709351</a>.","ista":"Schafzahl L, Mahne N, Schafzahl B, Wilkening M, Slugovc C, Borisov SM, Freunberger SA. 2017. Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. Angewandte Chemie. 129(49), 15934–15938.","mla":"Schafzahl, Lukas, et al. “Singulett-Sauerstoff in Der Aprotischen Natrium-O2-Batterie.” <i>Angewandte Chemie</i>, vol. 129, no. 49, Wiley, 2017, pp. 15934–38, doi:<a href=\"https://doi.org/10.1002/ange.201709351\">10.1002/ange.201709351</a>.","apa":"Schafzahl, L., Mahne, N., Schafzahl, B., Wilkening, M., Slugovc, C., Borisov, S. M., &#38; Freunberger, S. A. (2017). Singulett-Sauerstoff in der aprotischen Natrium-O2-Batterie. <i>Angewandte Chemie</i>. Wiley. <a href=\"https://doi.org/10.1002/ange.201709351\">https://doi.org/10.1002/ange.201709351</a>"}},{"has_accepted_license":"1","doi":"10.1038/nenergy.2017.91","language":[{"iso":"eng"}],"day":"05","oa_version":"Submitted Version","date_updated":"2021-01-12T08:16:20Z","type":"journal_article","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"publication_identifier":{"issn":["2058-7546"]},"file":[{"file_id":"8046","date_updated":"2020-07-14T12:48:06Z","checksum":"2564255b76f5346a32e764dbfd17fa2f","file_name":"NEnergy_Comment_final.pdf","access_level":"open_access","relation":"main_file","date_created":"2020-06-29T13:26:55Z","file_size":817665,"creator":"sfreunbe","content_type":"application/pdf"}],"external_id":{"arxiv":["2002.00712"]},"date_published":"2017-06-05T00:00:00Z","abstract":[{"lang":"eng","text":"Beyond-intercalation batteries promise a step-change in energy storage compared to intercalation-based lithium-ion and sodium-ion batteries. However, only performance metrics that include all cell components and operation parameters can tell whether a true advance over intercalation batteries has been achieved."}],"publication_status":"published","_id":"7982","ddc":["540","546","541"],"oa":1,"publication":"Nature Energy","title":"True performance metrics in beyond-intercalation batteries","year":"2017","quality_controlled":"1","author":[{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander"}],"extern":"1","citation":{"ista":"Freunberger SA. 2017. True performance metrics in beyond-intercalation batteries. Nature Energy. 2(7), 17091.","short":"S.A. Freunberger, Nature Energy 2 (2017).","chicago":"Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation Batteries.” <i>Nature Energy</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nenergy.2017.91\">https://doi.org/10.1038/nenergy.2017.91</a>.","ieee":"S. A. Freunberger, “True performance metrics in beyond-intercalation batteries,” <i>Nature Energy</i>, vol. 2, no. 7. Springer Nature, 2017.","ama":"Freunberger SA. True performance metrics in beyond-intercalation batteries. <i>Nature Energy</i>. 2017;2(7). doi:<a href=\"https://doi.org/10.1038/nenergy.2017.91\">10.1038/nenergy.2017.91</a>","mla":"Freunberger, Stefan Alexander. “True Performance Metrics in Beyond-Intercalation Batteries.” <i>Nature Energy</i>, vol. 2, no. 7, 17091, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/nenergy.2017.91\">10.1038/nenergy.2017.91</a>.","apa":"Freunberger, S. A. (2017). True performance metrics in beyond-intercalation batteries. <i>Nature Energy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nenergy.2017.91\">https://doi.org/10.1038/nenergy.2017.91</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/2002.00712","open_access":"1"}],"status":"public","article_number":"17091","month":"06","date_created":"2020-06-19T08:23:47Z","intvolume":"         2","publisher":"Springer Nature","article_type":"original","file_date_updated":"2020-07-14T12:48:06Z","issue":"7","volume":2},{"doi":"10.1038/nenergy.2017.36","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"20","oa_version":"Preprint","type":"journal_article","date_updated":"2021-01-12T08:16:21Z","publication_identifier":{"issn":["2058-7546"]},"arxiv":1,"external_id":{"arxiv":["1711.10340"]},"date_published":"2017-03-20T00:00:00Z","_id":"7986","oa":1,"title":"Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries","publication":"Nature Energy","publication_status":"published","extern":"1","quality_controlled":"1","author":[{"full_name":"Mahne, Nika","first_name":"Nika","last_name":"Mahne"},{"first_name":"Bettina","last_name":"Schafzahl","full_name":"Schafzahl, Bettina"},{"last_name":"Leypold","first_name":"Christian","full_name":"Leypold, Christian"},{"first_name":"Mario","last_name":"Leypold","full_name":"Leypold, Mario"},{"last_name":"Grumm","first_name":"Sandra","full_name":"Grumm, Sandra"},{"full_name":"Leitgeb, Anita","last_name":"Leitgeb","first_name":"Anita"},{"full_name":"Strohmeier, Gernot A.","first_name":"Gernot A.","last_name":"Strohmeier"},{"full_name":"Wilkening, Martin","first_name":"Martin","last_name":"Wilkening"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"},{"last_name":"Kramer","first_name":"Denis","full_name":"Kramer, Denis"},{"full_name":"Slugovc, Christian","last_name":"Slugovc","first_name":"Christian"},{"full_name":"Borisov, Sergey M.","first_name":"Sergey M.","last_name":"Borisov"},{"first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"citation":{"chicago":"Mahne, Nika, Bettina Schafzahl, Christian Leypold, Mario Leypold, Sandra Grumm, Anita Leitgeb, Gernot A. Strohmeier, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” <i>Nature Energy</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nenergy.2017.36\">https://doi.org/10.1038/nenergy.2017.36</a>.","short":"N. Mahne, B. Schafzahl, C. Leypold, M. Leypold, S. Grumm, A. Leitgeb, G.A. Strohmeier, M. Wilkening, O. Fontaine, D. Kramer, C. Slugovc, S.M. Borisov, S.A. Freunberger, Nature Energy 2 (2017).","ista":"Mahne N, Schafzahl B, Leypold C, Leypold M, Grumm S, Leitgeb A, Strohmeier GA, Wilkening M, Fontaine O, Kramer D, Slugovc C, Borisov SM, Freunberger SA. 2017. Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. Nature Energy. 2(5), 17036.","ama":"Mahne N, Schafzahl B, Leypold C, et al. Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. <i>Nature Energy</i>. 2017;2(5). doi:<a href=\"https://doi.org/10.1038/nenergy.2017.36\">10.1038/nenergy.2017.36</a>","ieee":"N. Mahne <i>et al.</i>, “Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries,” <i>Nature Energy</i>, vol. 2, no. 5. Springer Nature, 2017.","mla":"Mahne, Nika, et al. “Singlet Oxygen Generation as a Major Cause for Parasitic Reactions during Cycling of Aprotic Lithium–Oxygen Batteries.” <i>Nature Energy</i>, vol. 2, no. 5, 17036, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/nenergy.2017.36\">10.1038/nenergy.2017.36</a>.","apa":"Mahne, N., Schafzahl, B., Leypold, C., Leypold, M., Grumm, S., Leitgeb, A., … Freunberger, S. A. (2017). Singlet oxygen generation as a major cause for parasitic reactions during cycling of aprotic lithium–oxygen batteries. <i>Nature Energy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nenergy.2017.36\">https://doi.org/10.1038/nenergy.2017.36</a>"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.10340"}],"year":"2017","intvolume":"         2","status":"public","article_number":"17036 ","month":"03","date_created":"2020-06-19T10:42:33Z","volume":2,"issue":"5","publisher":"Springer Nature","article_type":"original"},{"year":"2017","citation":{"mla":"Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>, vol. 58, no. 10, 1801–1811, Oxford University Press, 2017, doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>.","apa":"Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima, K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>","ieee":"S. Kitakura <i>et al.</i>, “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,” <i>Plant and Cell Physiology</i>, vol. 58, no. 10. Oxford University Press, 2017.","ama":"Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. <i>Plant and Cell Physiology</i>. 2017;58(10). doi:<a href=\"https://doi.org/10.1093/pcp/pcx118\">10.1093/pcp/pcx118</a>","ista":"Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana. Plant and Cell Physiology. 58(10), 1801–1811.","chicago":"Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/pcp/pcx118\">https://doi.org/10.1093/pcp/pcx118</a>.","short":"S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima, C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017)."},"author":[{"full_name":"Kitakura, Saeko","first_name":"Saeko","last_name":"Kitakura"},{"first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257"},{"first_name":"Yuki","last_name":"Matsuura","full_name":"Matsuura, Yuki"},{"last_name":"Santuari","first_name":"Luca","full_name":"Santuari, Luca"},{"last_name":"Kouno","first_name":"Hirotaka","full_name":"Kouno, Hirotaka"},{"last_name":"Arima","first_name":"Kohei","full_name":"Arima, Kohei"},{"full_name":"Hardtke, Christian","last_name":"Hardtke","first_name":"Christian"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kakimoto, Tatsuo","first_name":"Tatsuo","last_name":"Kakimoto"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"}],"quality_controlled":"1","publication_status":"published","abstract":[{"text":"Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA), which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been revealed fully. In a previous study, we have identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2 as a crucial component of this BFA action at the level of TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.","lang":"eng"}],"title":"BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana","publication":"Plant and Cell Physiology","pmid":1,"oa":1,"ddc":["581"],"_id":"799","file_date_updated":"2020-07-14T12:48:06Z","publisher":"Oxford University Press","volume":58,"issue":"10","pubrep_id":"1009","date_created":"2018-12-11T11:48:34Z","month":"08","article_number":"1801-1811","status":"public","intvolume":"        58","publist_id":"6854","isi":1,"type":"journal_article","date_updated":"2023-09-27T11:00:19Z","oa_version":"Submitted Version","day":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1093/pcp/pcx118","department":[{"_id":"JiFr"}],"has_accepted_license":"1","date_published":"2017-08-21T00:00:00Z","file":[{"relation":"main_file","date_created":"2019-04-17T07:52:34Z","creator":"dernst","content_type":"application/pdf","file_size":1352913,"date_updated":"2020-07-14T12:48:06Z","file_id":"6333","checksum":"bd3e3a94d55416739cbb19624bb977f8","file_name":"2017_PlantCellPhysio_Kitakura.pdf","access_level":"open_access"}],"external_id":{"isi":["000413220400019"],"pmid":["29016942"]},"publication_identifier":{"issn":["00320781"]},"scopus_import":"1"}]