[{"citation":{"apa":"Borge, M., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., &#38; Ford, B. (2017). Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. Paris, France: IEEE. <a href=\"https://doi.org/10.1109/eurospw.2017.46\">https://doi.org/10.1109/eurospw.2017.46</a>","ama":"Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In: <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/eurospw.2017.46\">10.1109/eurospw.2017.46</a>","short":"M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, B. Ford, in:, 2017 IEEE European Symposium on Security and Privacy Workshops, IEEE, 2017.","mla":"Borge, Maria, et al. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>, 7966966, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/eurospw.2017.46\">10.1109/eurospw.2017.46</a>.","ieee":"M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, and B. Ford, “Proof-of-personhood: Redemocratizing permissionless cryptocurrencies,” in <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>, Paris, France, 2017.","ista":"Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. 2017. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. 2017 IEEE European Symposium on Security and Privacy Workshops. EuroS&#38;PW: European Symposium on Security and Privacy Workshops, 7966966.","chicago":"Borge, Maria, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, and Bryan Ford. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” In <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/eurospw.2017.46\">https://doi.org/10.1109/eurospw.2017.46</a>."},"title":"Proof-of-personhood: Redemocratizing permissionless cryptocurrencies","conference":{"name":"EuroS&PW: European Symposium on Security and Privacy Workshops","start_date":"2017-04-26","end_date":"2017-04-28","location":"Paris, France"},"day":"30","type":"conference","author":[{"full_name":"Borge, Maria","first_name":"Maria","last_name":"Borge"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Jovanovic","full_name":"Jovanovic, Philipp","first_name":"Philipp"},{"last_name":"Gasser","first_name":"Linus","full_name":"Gasser, Linus"},{"first_name":"Nicolas","full_name":"Gailly, Nicolas","last_name":"Gailly"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"oa_version":"None","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:17:57Z","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781538622445"]},"doi":"10.1109/eurospw.2017.46","article_processing_charge":"No","month":"06","extern":"1","article_number":"7966966","date_created":"2020-08-26T11:48:11Z","_id":"8299","date_published":"2017-06-30T00:00:00Z","abstract":[{"lang":"eng","text":"Permissionless blockchain-based cryptocurrencies commonly use proof-of-work (PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double spending attacks. However, both approaches have disadvantages: PoW leads to massive amounts of wasted electricity and re-centralization, whereas major stakeholders in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood (PoP), a mechanism that binds physical entities to virtual identities in a way that enables accountability while preserving anonymity. Afterwards we introduce PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a continuously fair and democratic wealth creation process which paves the way for an experimental basic income infrastructure."}],"publication_status":"published","publisher":"IEEE","publication":"2017 IEEE European Symposium on Security and Privacy Workshops","quality_controlled":"1","status":"public"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf"}],"publication_status":"published","publisher":"USENIX Association","status":"public","quality_controlled":"1","publication":"Proceedings of the 26th USENIX Conference on Security Symposium","article_processing_charge":"No","page":"1271–1287","abstract":[{"lang":"eng","text":"Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that eliminates single points of failure, enforces transparency, and provides efficient verifiability of integrity and authenticity for software-release processes. Independent witness servers collectively verify conformance of software updates to release policies, build verifiers validate the source-to-binary correspondence, and a tamper-proof release log stores collectively signed updates, thus ensuring that no release is accepted by clients before being widely disclosed and validated. The release log embodies a skipchain, a novel data structure, enabling arbitrarily out-of-date clients to efficiently validate updates and signing keys. Evaluation of our CHAINIAC prototype on reproducible Debian packages shows that the automated update process takes the average of 5 minutes per release for individual packages, and only 20 seconds for the aggregate timeline. We further evaluate the framework using real-world data from the PyPI package repository and show that it offers clients security comparable to verifying every single update themselves while consuming only one-fifth of the bandwidth and having a minimal computational overhead."}],"_id":"8301","date_published":"2017-09-01T00:00:00Z","date_created":"2020-08-26T12:04:44Z","extern":"1","month":"09","publication_identifier":{"isbn":["9781931971409"]},"date_updated":"2021-01-12T08:18:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"location":"Vancouver, Canada","start_date":"2017-08-16","end_date":"2017-08-18","name":"SEC: Security Symposium"},"title":"CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds","citation":{"mla":"Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, USENIX Association, 2017, pp. 1271–1287.","chicago":"Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” In <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, 1271–1287. USENIX Association, 2017.","ista":"Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. Proceedings of the 26th USENIX Conference on Security Symposium. SEC: Security Symposium, 1271–1287.","ieee":"K. Nikitin <i>et al.</i>, “CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds,” in <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, Vancouver, Canada, 2017, pp. 1271–1287.","ama":"Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In: <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>. USENIX Association; 2017:1271–1287.","apa":"Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi, I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In <i>Proceedings of the 26th USENIX Conference on Security Symposium</i> (pp. 1271–1287). Vancouver, Canada: USENIX Association.","short":"K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi, J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287."},"oa_version":"Published Version","year":"2017","type":"conference","author":[{"full_name":"Nikitin, Kirill","first_name":"Kirill","last_name":"Nikitin"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Jovanovic","first_name":"Philipp","full_name":"Jovanovic, Philipp"},{"last_name":"Gasser","full_name":"Gasser, Linus","first_name":"Linus"},{"last_name":"Gailly","full_name":"Gailly, Nicolas","first_name":"Nicolas"},{"last_name":"Khoffi","first_name":"Ismail","full_name":"Khoffi, Ismail"},{"last_name":"Cappos","full_name":"Cappos, Justin","first_name":"Justin"},{"full_name":"Ford, Bryan","first_name":"Bryan","last_name":"Ford"}],"day":"01"},{"day":"01","year":"2017","oa_version":"Preprint","author":[{"first_name":"E.","full_name":"Syta, E.","last_name":"Syta"},{"last_name":"Jovanovic","full_name":"Jovanovic, P.","first_name":"P."},{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"N.","full_name":"Gailly, N.","last_name":"Gailly"},{"full_name":"Gasser, L.","first_name":"L.","last_name":"Gasser"},{"full_name":"Khoffi, I.","first_name":"I.","last_name":"Khoffi"},{"last_name":"Fischer","first_name":"M. J.","full_name":"Fischer, M. J."},{"first_name":"B.","full_name":"Ford, B.","last_name":"Ford"}],"type":"conference","citation":{"ieee":"E. Syta <i>et al.</i>, “Scalable bias-resistant distributed randomness,” in <i>2017 IEEE Symposium on Security and Privacy</i>, San Jose, CA, United States, 2017, pp. 444–460.","ista":"Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 444–460.","chicago":"Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.” In <i>2017 IEEE Symposium on Security and Privacy</i>, 444–60. IEEE, 2017. <a href=\"https://doi.org/10.1109/SP.2017.45\">https://doi.org/10.1109/SP.2017.45</a>.","mla":"Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” <i>2017 IEEE Symposium on Security and Privacy</i>, IEEE, 2017, pp. 444–60, doi:<a href=\"https://doi.org/10.1109/SP.2017.45\">10.1109/SP.2017.45</a>.","short":"E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–460.","apa":"Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi, I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In <i>2017 IEEE Symposium on Security and Privacy</i> (pp. 444–460). San Jose, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/SP.2017.45\">https://doi.org/10.1109/SP.2017.45</a>","ama":"Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed randomness. In: <i>2017 IEEE Symposium on Security and Privacy</i>. IEEE; 2017:444-460. doi:<a href=\"https://doi.org/10.1109/SP.2017.45\">10.1109/SP.2017.45</a>"},"conference":{"name":"SP: Symposium on Security and Privacy","end_date":"2017-05-26","start_date":"2017-05-22","location":"San Jose, CA, United States"},"title":"Scalable bias-resistant distributed randomness","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:18:02Z","doi":"10.1109/SP.2017.45","publication_identifier":{"isbn":["9781509055340"],"issn":["2375-1207"]},"extern":"1","month":"06","date_published":"2017-06-01T00:00:00Z","_id":"8306","date_created":"2020-08-26T12:26:08Z","abstract":[{"text":"Bias-resistant public randomness is a critical component in many (distributed) protocols. Generating public randomness is hard, however, because active adversaries may behave dishonestly to bias public random choices toward their advantage. Existing solutions do not scale to hundreds or thousands of participants, as is needed in many decentralized systems. We propose two large-scale distributed protocols, RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted client to divide a set of randomness servers into groups for scalability, and it depends on the pigeonhole principle to ensure output integrity, even for non-random, adversarial group choices. RandHerd implements an efficient, decentralized randomness beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound in a one-time setup to arrange participants into verifiably unbiased random secret-sharing groups, which then repeatedly produce random output at predefined intervals. Our prototype demonstrates that RandHound and RandHerd achieve good performance across hundreds of participants while retaining a low failure probability by properly selecting protocol parameters, such as a group size and secret-sharing threshold. For example, when sharding 512 nodes into groups of 32, our experiments show that RandHound can produce fresh random output after 240 seconds. RandHerd, after a setup phase of 260 seconds, is able to generate fresh random output in intervals of approximately 6 seconds. For this configuration, both protocols operate at a failure probability of at most 0.08% against a Byzantine adversary.","lang":"eng"}],"page":"444-460","article_processing_charge":"No","quality_controlled":"1","publication":"2017 IEEE Symposium on Security and Privacy","status":"public","publisher":"IEEE","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1067"}],"oa":1},{"intvolume":"     10424","status":"public","department":[{"_id":"HeEd"}],"quality_controlled":"1","isi":1,"publisher":"Springer","date_created":"2018-12-11T11:48:45Z","month":"07","page":"397 - 409","doi":"10.1007/978-3-319-64689-3_32","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"type":"conference","author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","first_name":"Teresa","full_name":"Heiss, Teresa","last_name":"Heiss"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"day":"28","conference":{"location":"Ystad, Sweden","end_date":"2017-08-24","start_date":"2017-08-22","name":"CAIP: Computer Analysis of Images and Patterns"},"title":"Streaming algorithm for Euler characteristic curves of multidimensional images","citation":{"apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>."},"volume":10424,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.02045","open_access":"1"}],"publication_status":"published","_id":"833","date_published":"2017-07-28T00:00:00Z","abstract":[{"text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams.","lang":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["03029743"]},"date_updated":"2023-09-26T16:10:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","external_id":{"isi":["000432085900032"]},"oa_version":"Submitted Version","year":"2017","publist_id":"6815","editor":[{"last_name":"Felsberg","full_name":"Felsberg, Michael","first_name":"Michael"},{"last_name":"Heyden","first_name":"Anders","full_name":"Heyden, Anders"},{"last_name":"Krüger","full_name":"Krüger, Norbert","first_name":"Norbert"}]},{"date_created":"2018-12-11T11:48:45Z","month":"09","intvolume":"        96","status":"public","publication":"Physical Review B - Condensed Matter and Materials Physics","department":[{"_id":"MaSe"}],"quality_controlled":"1","isi":1,"publisher":"American Physical Society","type":"journal_article","author":[{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Papic","full_name":"Zlatko, Papic","last_name":"Zlatko"},{"last_name":"Abanin","first_name":"Dmitry","full_name":"Abanin, Dmitry"}],"day":"06","title":"Thouless energy and multifractality across the many-body localization transition","citation":{"short":"M. Serbyn, P. Zlatko, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017).","ama":"Serbyn M, Zlatko P, Abanin D. Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2017;96(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>","apa":"Serbyn, M., Zlatko, P., &#38; Abanin, D. (2017). Thouless energy and multifractality across the many-body localization transition. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>","chicago":"Serbyn, Maksym, Papic Zlatko, and Dmitry Abanin. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">https://doi.org/10.1103/PhysRevB.96.104201</a>.","ieee":"M. Serbyn, P. Zlatko, and D. Abanin, “Thouless energy and multifractality across the many-body localization transition,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10. American Physical Society, 2017.","ista":"Serbyn M, Zlatko P, Abanin D. 2017. Thouless energy and multifractality across the many-body localization transition. Physical Review B - Condensed Matter and Materials Physics. 96(10), 104201.","mla":"Serbyn, Maksym, et al. “Thouless Energy and Multifractality across the Many-Body Localization Transition.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 96, no. 10, 104201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevB.96.104201\">10.1103/PhysRevB.96.104201</a>."},"doi":"10.1103/PhysRevB.96.104201","language":[{"iso":"eng"}],"acknowledgement":"We   acknowledge   useful   discussions with V. Kravtsov, T. Grover, and R. Vasseur.  M.S. was supported by Gordon and Betty Moore Foundation’s EPiQS Initiative through Grant GBMF4307.  M.S. and D.A.  acknowledge  hospitality  of  KITP,  where  parts  of this work were completed (supported in part by the National Science Foundation under Grant No. NSF PHY11-25915)","_id":"834","abstract":[{"lang":"eng","text":"Thermal and many-body localized phases are separated by a dynamical phase transition of a new kind. We analyze the distribution of off-diagonal matrix elements of local operators across this transition in two different models of disordered spin chains. We show that the behavior of matrix elements can be used to characterize the breakdown of thermalization and to extract the many-body Thouless energy. We find that upon increasing the disorder strength the system enters a critical region around the many-body localization transition. The properties of the system in this region are: (i) the Thouless energy becomes smaller than the level spacing, (ii) the matrix elements show critical dependence on the energy difference, and (iii) the matrix elements, viewed as amplitudes of a fictitious wave function, exhibit strong multifractality. This critical region decreases with the system size, which we interpret as evidence for a diverging correlation length at the many-body localization transition. Our findings show that the correlation length becomes larger than the accessible system sizes in a broad range of disorder strength values and shed light on the critical behavior near the many-body localization transition."}],"date_published":"2017-09-06T00:00:00Z","article_number":"104201","article_processing_charge":"No","issue":"10","volume":96,"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02389"}],"publication_status":"published","oa_version":"Submitted Version","year":"2017","publist_id":"6814","publication_identifier":{"issn":["24699950"]},"scopus_import":"1","external_id":{"isi":["000409429300004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:51:54Z"},{"day":"27","author":[{"last_name":"Makhijani","full_name":"Makhijani, Kalpana","first_name":"Kalpana"},{"last_name":"Alexander","first_name":"Brandy","full_name":"Alexander, Brandy"},{"full_name":"Rao, Deepti","first_name":"Deepti","last_name":"Rao"},{"first_name":"Sophia","full_name":"Petraki, Sophia","last_name":"Petraki"},{"last_name":"Herboso","first_name":"Leire","full_name":"Herboso, Leire"},{"first_name":"Katelyn","full_name":"Kukar, Katelyn","last_name":"Kukar"},{"full_name":"Batool, Itrat","first_name":"Itrat","last_name":"Batool"},{"first_name":"Stephanie","full_name":"Wachner, Stephanie","last_name":"Wachner","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gold","first_name":"Katrina","full_name":"Gold, Katrina"},{"last_name":"Wong","first_name":"Corinna","full_name":"Wong, Corinna"},{"last_name":"O'Connor","full_name":"O'Connor, Michael","first_name":"Michael"},{"last_name":"Brückner","full_name":"Brückner, Katja","first_name":"Katja"}],"type":"journal_article","citation":{"ama":"Makhijani K, Alexander B, Rao D, et al. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15990\">10.1038/ncomms15990</a>","apa":"Makhijani, K., Alexander, B., Rao, D., Petraki, S., Herboso, L., Kukar, K., … Brückner, K. (2017). Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15990\">https://doi.org/10.1038/ncomms15990</a>","short":"K. Makhijani, B. Alexander, D. Rao, S. Petraki, L. Herboso, K. Kukar, I. Batool, S. Wachner, K. Gold, C. Wong, M. O’Connor, K. Brückner, Nature Communications 8 (2017).","mla":"Makhijani, Kalpana, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” <i>Nature Communications</i>, vol. 8, 15990, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15990\">10.1038/ncomms15990</a>.","chicago":"Makhijani, Kalpana, Brandy Alexander, Deepti Rao, Sophia Petraki, Leire Herboso, Katelyn Kukar, Itrat Batool, et al. “Regulation of Drosophila Hematopoietic Sites by Activin-β from Active Sensory Neurons.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15990\">https://doi.org/10.1038/ncomms15990</a>.","ieee":"K. Makhijani <i>et al.</i>, “Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ista":"Makhijani K, Alexander B, Rao D, Petraki S, Herboso L, Kukar K, Batool I, Wachner S, Gold K, Wong C, O’Connor M, Brückner K. 2017. Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons. Nature Communications. 8, 15990."},"title":"Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons","language":[{"iso":"eng"}],"doi":"10.1038/ncomms15990","ddc":["570","576","616"],"extern":"1","month":"07","date_created":"2018-12-11T11:48:45Z","quality_controlled":"1","publication":"Nature Communications","intvolume":"         8","status":"public","publisher":"Nature Publishing Group","isi":1,"publist_id":"6813","oa_version":"Published Version","has_accepted_license":"1","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-26T15:51:28Z","external_id":{"isi":["000406360100001"]},"publication_identifier":{"issn":["20411723"]},"file":[{"date_created":"2018-12-12T10:15:32Z","file_id":"5153","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:12Z","checksum":"99a3d63308d4250eda0a35341171f80e","creator":"system","file_size":3027104,"file_name":"IST-2017-859-v1+1_ncomms15990.pdf"}],"article_number":"15990","abstract":[{"text":"An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined.","lang":"eng"}],"_id":"835","date_published":"2017-07-27T00:00:00Z","article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:12Z","volume":8,"pubrep_id":"859","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1},{"author":[{"full_name":"Ethier, Marc","first_name":"Marc","last_name":"Ethier"},{"orcid":"0000-0002-3536-9866","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","first_name":"Grzegorz","full_name":"Jablonski, Grzegorz","last_name":"Jablonski"},{"first_name":"Marian","full_name":"Mrozek, Marian","last_name":"Mrozek"}],"type":"conference","alternative_title":["PROMS"],"day":"27","title":"Finding eigenvalues of self-maps with the Kronecker canonical form","conference":{"location":"Kalamata, Greece","end_date":"2015-07-23","start_date":"2015-07-20","name":"ACA: Applications of Computer Algebra"},"citation":{"short":"M. Ethier, G. Jablonski, M. Mrozek, in:, Special Sessions in Applications of Computer Algebra, Springer, 2017, pp. 119–136.","ama":"Ethier M, Jablonski G, Mrozek M. Finding eigenvalues of self-maps with the Kronecker canonical form. In: <i>Special Sessions in Applications of Computer Algebra</i>. Vol 198. Springer; 2017:119-136. doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>","apa":"Ethier, M., Jablonski, G., &#38; Mrozek, M. (2017). Finding eigenvalues of self-maps with the Kronecker canonical form. In <i>Special Sessions in Applications of Computer Algebra</i> (Vol. 198, pp. 119–136). Kalamata, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>","chicago":"Ethier, Marc, Grzegorz Jablonski, and Marian Mrozek. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” In <i>Special Sessions in Applications of Computer Algebra</i>, 198:119–36. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">https://doi.org/10.1007/978-3-319-56932-1_8</a>.","ieee":"M. Ethier, G. Jablonski, and M. Mrozek, “Finding eigenvalues of self-maps with the Kronecker canonical form,” in <i>Special Sessions in Applications of Computer Algebra</i>, Kalamata, Greece, 2017, vol. 198, pp. 119–136.","ista":"Ethier M, Jablonski G, Mrozek M. 2017. Finding eigenvalues of self-maps with the Kronecker canonical form. Special Sessions in Applications of Computer Algebra. ACA: Applications of Computer Algebra, PROMS, vol. 198, 119–136.","mla":"Ethier, Marc, et al. “Finding Eigenvalues of Self-Maps with the Kronecker Canonical Form.” <i>Special Sessions in Applications of Computer Algebra</i>, vol. 198, Springer, 2017, pp. 119–36, doi:<a href=\"https://doi.org/10.1007/978-3-319-56932-1_8\">10.1007/978-3-319-56932-1_8</a>."},"ec_funded":1,"doi":"10.1007/978-3-319-56932-1_8","language":[{"iso":"eng"}],"project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:48:46Z","month":"07","page":"119 - 136","intvolume":"       198","status":"public","publication":"Special Sessions in Applications of Computer Algebra","quality_controlled":"1","department":[{"_id":"HeEd"}],"isi":1,"publisher":"Springer","year":"2017","oa_version":"None","publist_id":"6812","publication_identifier":{"isbn":["978-331956930-7"]},"external_id":{"isi":["000434088200008"]},"scopus_import":"1","date_updated":"2023-09-26T15:50:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2017-07-27T00:00:00Z","_id":"836","abstract":[{"lang":"eng","text":"Recent research has examined how to study the topological features of a continuous self-map by means of the persistence of the eigenspaces, for given eigenvalues, of the endomorphism induced in homology over a field. This raised the question of how to select dynamically significant eigenvalues. The present paper aims to answer this question, giving an algorithm that computes the persistence of eigenspaces for every eigenvalue simultaneously, also expressing said eigenspaces as direct sums of “finite” and “singular” subspaces."}],"article_processing_charge":"No","volume":198,"publication_status":"published"},{"doi":"10.15479/AT:ISTA:th_858","ddc":["571"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5828"}]},"acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","type":"dissertation","author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","full_name":"Xu, Haibing","last_name":"Xu"}],"alternative_title":["ISTA Thesis"],"day":"23","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","citation":{"short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>."},"status":"public","department":[{"_id":"JoCs"}],"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"}],"date_created":"2018-12-11T11:48:46Z","month":"08","page":"93","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:06:38Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","has_accepted_license":"1","year":"2017","publist_id":"6811","pubrep_id":"858","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:12Z","oa":1,"publication_status":"published","_id":"837","date_published":"2017-08-23T00:00:00Z","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:12Z","access_level":"closed","checksum":"f11925fbbce31e495124b6bc4f10573c","file_name":"2017_Xu_Haibing_Thesis_Source.docx","file_size":3589490,"creator":"dernst","date_created":"2019-04-05T08:59:51Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_id":"6213"},{"content_type":"application/pdf","relation":"main_file","file_id":"6214","date_created":"2019-04-05T08:59:51Z","file_name":"2017_Xu_Thesis_IST.pdf","creator":"dernst","file_size":11668613,"checksum":"ffb10749a537d615fab1ef0937ccb157","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access"}],"article_processing_charge":"No"},{"publist_id":"6810","has_accepted_license":"1","year":"2017","oa_version":"Published Version","date_updated":"2023-09-07T12:02:28Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","file":[{"file_size":847400,"creator":"system","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:12Z","checksum":"ff8639ec4bded6186f44c7bd3ee26804","relation":"main_file","file_id":"4799","content_type":"application/pdf","date_created":"2018-12-12T10:10:13Z"},{"file_size":26054879,"creator":"dernst","file_name":"2017_Thesis_Rybar_source.zip","checksum":"3462101745ce8ad199c2d0f75dae4a7e","access_level":"closed","date_updated":"2020-07-14T12:48:12Z","file_id":"6202","relation":"source_file","content_type":"application/zip","date_created":"2019-04-05T08:24:11Z"}],"_id":"838","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"date_published":"2017-06-26T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:12Z","pubrep_id":"828","citation":{"short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>."},"title":"(The exact security of) Message authentication codes","day":"26","alternative_title":["ISTA Thesis"],"author":[{"first_name":"Michal","full_name":"Rybar, Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","related_material":{"record":[{"status":"public","id":"2082","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6196","status":"public"}]},"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_828","ddc":["000"],"page":"86","month":"06","date_created":"2018-12-11T11:48:46Z","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"KrPi"}],"status":"public"},{"publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-02-21T13:48:02Z","year":"2017","has_accepted_license":"1","oa_version":"Published Version","publist_id":"6809","oa":1,"publication_status":"published","license":"https://creativecommons.org/licenses/by-sa/4.0/","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"pubrep_id":"855","file_date_updated":"2020-07-14T12:48:13Z","article_processing_charge":"No","abstract":[{"text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. ","lang":"eng"}],"_id":"839","date_published":"2017-08-14T00:00:00Z","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"5100","date_created":"2018-12-12T10:14:46Z","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","file_size":14596191,"creator":"system","date_updated":"2020-07-14T12:48:13Z","access_level":"open_access","checksum":"6c1ae8c90bfaba5e089417fefbc4a272"},{"file_name":"2017_thesis_Hahn_source.zip","creator":"dernst","file_size":15060566,"checksum":"421672f68d563b029869c5cf1713f919","date_updated":"2020-07-14T12:48:13Z","access_level":"closed","content_type":"application/zip","file_id":"6207","relation":"source_file","date_created":"2019-04-05T08:40:30Z"}],"acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","related_material":{"record":[{"id":"1362","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"1633","relation":"part_of_dissertation"},{"status":"public","relation":"popular_science","id":"5568"}]},"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"ddc":["004","005","006","531","621"],"doi":"10.15479/AT:ISTA:th_855","language":[{"iso":"eng"}],"title":"Brittle fracture simulation with boundary elements for computer graphics","ec_funded":1,"citation":{"ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria.","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>"},"alternative_title":["ISTA Thesis"],"type":"dissertation","author":[{"first_name":"David","full_name":"Hahn, David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"}],"day":"14","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"ChWo"}],"page":"124","date_created":"2018-12-11T11:48:47Z","supervisor":[{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"month":"08"},{"article_processing_charge":"No","page":"1709 - 1735","_id":"84","abstract":[{"text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.","lang":"eng"}],"date_published":"2017-11-09T00:00:00Z","date_created":"2018-12-11T11:44:32Z","series_title":"Handbook of Discrete and Computational Geometry","month":"11","publication_status":"published","publisher":"Taylor & Francis","status":"public","department":[{"_id":"HeEd"}],"quality_controlled":"1","publication":"Handbook of Discrete and Computational Geometry, Third Edition","editor":[{"full_name":"Toth, Csaba","first_name":"Csaba","last_name":"Toth"},{"last_name":"O'Rourke","first_name":"Joseph","full_name":"O'Rourke, Joseph"},{"first_name":"Jacob","full_name":"Goodman, Jacob","last_name":"Goodman"}],"title":"Computational topology for structural molecular biology","citation":{"chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735.","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735.","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>","apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>"},"year":"2017","oa_version":"None","type":"book_chapter","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Patrice","full_name":"Koehl, Patrice","last_name":"Koehl"}],"day":"09","publist_id":"7970","doi":"10.1201/9781315119601","publication_identifier":{"eisbn":["9781498711425"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-10-16T11:15:22Z","scopus_import":"1"},{"has_accepted_license":"1","oa_version":"Published Version","year":"2017","publist_id":"6808","publication_identifier":{"issn":["15306984"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"date_updated":"2023-09-26T15:50:22Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000411043500078"]},"scopus_import":"1","issue":"9","article_processing_charge":"No","_id":"840","abstract":[{"text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.","lang":"eng"}],"date_published":"2017-08-10T00:00:00Z","file":[{"content_type":"application/pdf","file_id":"4951","relation":"main_file","date_created":"2018-12-12T10:12:33Z","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf","file_size":2449546,"creator":"system","date_updated":"2020-07-14T12:48:13Z","access_level":"open_access","checksum":"761371a0129b2aa442424b9561450ece"}],"oa":1,"publication_status":"published","volume":17,"pubrep_id":"865","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:13Z","title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","ec_funded":1,"citation":{"chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>.","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” <i>Nano Letters</i>, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>.","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. 2017;17(9):5706-5710. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>","apa":"Vukušić, L., Kukucka, J., Watzinger, H., &#38; Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>"},"author":[{"first_name":"Lada","full_name":"Vukusic, Lada","last_name":"Vukusic","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Watzinger","full_name":"Watzinger, Hannes","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georgios","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X"}],"type":"journal_article","day":"10","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"69","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"project":[{"call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"}],"ddc":["539"],"doi":"10.1021/acs.nanolett.7b02627","language":[{"iso":"eng"}],"page":"5706 - 5710","date_created":"2018-12-11T11:48:47Z","month":"08","isi":1,"publisher":"American Chemical Society","status":"public","intvolume":"        17","department":[{"_id":"GeKa"}],"quality_controlled":"1","publication":"Nano Letters"},{"page":"175-209","date_created":"2020-09-17T10:42:42Z","month":"12","extern":"1","publisher":"Duke University Press","intvolume":"       167","status":"public","publication":"Duke Mathematical Journal","quality_controlled":"1","title":"On the marked length spectrum of generic strictly convex billiard tables","citation":{"short":"G. Huang, V. Kaloshin, A. Sorrentino, Duke Mathematical Journal 167 (2017) 175–209.","ama":"Huang G, Kaloshin V, Sorrentino A. On the marked length spectrum of generic strictly convex billiard tables. <i>Duke Mathematical Journal</i>. 2017;167(1):175-209. doi:<a href=\"https://doi.org/10.1215/00127094-2017-0038\">10.1215/00127094-2017-0038</a>","apa":"Huang, G., Kaloshin, V., &#38; Sorrentino, A. (2017). On the marked length spectrum of generic strictly convex billiard tables. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2017-0038\">https://doi.org/10.1215/00127094-2017-0038</a>","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” <i>Duke Mathematical Journal</i>. Duke University Press, 2017. <a href=\"https://doi.org/10.1215/00127094-2017-0038\">https://doi.org/10.1215/00127094-2017-0038</a>.","ista":"Huang G, Kaloshin V, Sorrentino A. 2017. On the marked length spectrum of generic strictly convex billiard tables. Duke Mathematical Journal. 167(1), 175–209.","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “On the marked length spectrum of generic strictly convex billiard tables,” <i>Duke Mathematical Journal</i>, vol. 167, no. 1. Duke University Press, pp. 175–209, 2017.","mla":"Huang, Guan, et al. “On the Marked Length Spectrum of Generic Strictly Convex Billiard Tables.” <i>Duke Mathematical Journal</i>, vol. 167, no. 1, Duke University Press, 2017, pp. 175–209, doi:<a href=\"https://doi.org/10.1215/00127094-2017-0038\">10.1215/00127094-2017-0038</a>."},"author":[{"last_name":"Huang","first_name":"Guan","full_name":"Huang, Guan"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"last_name":"Sorrentino","full_name":"Sorrentino, Alfonso","first_name":"Alfonso"}],"type":"journal_article","day":"08","doi":"10.1215/00127094-2017-0038","language":[{"iso":"eng"}],"article_processing_charge":"No","issue":"1","arxiv":1,"abstract":[{"lang":"eng","text":"In this paper we show that for a generic strictly convex domain, one can recover the eigendata corresponding to Aubry–Mather periodic orbits of the induced billiard map from the (maximal) marked length spectrum of the domain."}],"_id":"8423","date_published":"2017-12-08T00:00:00Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.08838"}],"publication_status":"published","volume":167,"year":"2017","oa_version":"Preprint","article_type":"original","publication_identifier":{"issn":["0012-7094"]},"external_id":{"arxiv":["1603.08838"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:11Z"},{"publication":"Annals of Mathematics","quality_controlled":"1","status":"public","intvolume":"       186","publisher":"Annals of Mathematics","month":"07","extern":"1","date_created":"2020-09-17T10:46:42Z","page":"277-314","language":[{"iso":"eng"}],"doi":"10.4007/annals.2017.186.1.7","day":"01","type":"journal_article","author":[{"first_name":"Jacopo","full_name":"De Simoi, Jacopo","last_name":"De Simoi"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"first_name":"Qiaoling","full_name":"Wei, Qiaoling","last_name":"Wei"}],"citation":{"ista":"De Simoi J, Kaloshin V, Wei Q. 2017. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. Annals of Mathematics. 186(1), 277–314.","ieee":"J. De Simoi, V. Kaloshin, and Q. Wei, “Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle,” <i>Annals of Mathematics</i>, vol. 186, no. 1. Annals of Mathematics, pp. 277–314, 2017.","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Qiaoling Wei. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” <i>Annals of Mathematics</i>. Annals of Mathematics, 2017. <a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">https://doi.org/10.4007/annals.2017.186.1.7</a>.","mla":"De Simoi, Jacopo, et al. “Dynamical Spectral Rigidity among Z2-Symmetric Strictly Convex Domains Close to a Circle.” <i>Annals of Mathematics</i>, vol. 186, no. 1, Annals of Mathematics, 2017, pp. 277–314, doi:<a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">10.4007/annals.2017.186.1.7</a>.","short":"J. De Simoi, V. Kaloshin, Q. Wei, Annals of Mathematics 186 (2017) 277–314.","apa":"De Simoi, J., Kaloshin, V., &#38; Wei, Q. (2017). Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. <i>Annals of Mathematics</i>. Annals of Mathematics. <a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">https://doi.org/10.4007/annals.2017.186.1.7</a>","ama":"De Simoi J, Kaloshin V, Wei Q. Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle. <i>Annals of Mathematics</i>. 2017;186(1):277-314. doi:<a href=\"https://doi.org/10.4007/annals.2017.186.1.7\">10.4007/annals.2017.186.1.7</a>"},"title":"Dynamical spectral rigidity among Z2-symmetric strictly convex domains close to a circle","volume":186,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.00230"}],"oa":1,"_id":"8427","abstract":[{"lang":"eng","text":"We show that any sufficiently (finitely) smooth ℤ₂-symmetric strictly convex domain sufficiently close to a circle is dynamically spectrally rigid; i.e., all deformations among domains in the same class that preserve the length of all periodic orbits of the associated billiard flow must necessarily be isometric deformations. This gives a partial answer to a question of P. Sarnak."}],"date_published":"2017-07-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","issue":"1","external_id":{"arxiv":["1606.00230"]},"date_updated":"2021-01-12T08:19:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0003-486X"]},"article_type":"original","year":"2017","oa_version":"Preprint"},{"intvolume":"       113","status":"public","volume":113,"publication":"Biophysical Journal","quality_controlled":"1","publisher":"Elsevier","publication_status":"published","_id":"8444","date_published":"2017-12-05T00:00:00Z","abstract":[{"lang":"eng","text":"Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment."}],"date_created":"2020-09-18T10:05:54Z","month":"12","extern":"1","article_processing_charge":"No","issue":"11","page":"2311-2315","publication_identifier":{"issn":["0006-3495"]},"doi":"10.1016/j.bpj.2017.09.019","keyword":["Biophysics"],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:18Z","author":[{"first_name":"François","full_name":"Dehez, François","last_name":"Dehez"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"Martin S.","full_name":"King, Martin S.","last_name":"King"},{"first_name":"Edmund R.S.","full_name":"Kunji, Edmund R.S.","last_name":"Kunji"},{"full_name":"Chipot, Christophe","first_name":"Christophe","last_name":"Chipot"}],"type":"journal_article","oa_version":"None","year":"2017","article_type":"original","day":"05","title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","citation":{"apa":"Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., &#38; Chipot, C. (2017). Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>","ama":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. 2017;113(11):2311-2315. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315.","mla":"Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>, vol. 113, no. 11, Elsevier, 2017, pp. 2311–15, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>.","ieee":"F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,” <i>Biophysical Journal</i>, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.","ista":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 113(11), 2311–2315.","chicago":"Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>."}},{"article_processing_charge":"No","article_number":"145","extern":"1","month":"07","_id":"8445","abstract":[{"text":"Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch–McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3–5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.","lang":"eng"}],"date_published":"2017-07-27T00:00:00Z","date_created":"2020-09-18T10:06:01Z","publisher":"Springer Nature","publication_status":"published","quality_controlled":"1","publication":"Nature Communications","volume":8,"status":"public","intvolume":"         8","citation":{"mla":"Kurauskas, Vilius, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>, vol. 8, 145, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>.","ieee":"V. Kurauskas <i>et al.</i>, “Slow conformational exchange and overall rocking motion in ubiquitin protein crystals,” <i>Nature Communications</i>, vol. 8. Springer Nature, 2017.","ista":"Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier J-P, Skrynnikov NR, Schanda P. 2017. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 8, 145.","chicago":"Kurauskas, Vilius, Sergei A. Izmailov, Olga N. Rogacheva, Audrey Hessel, Isabel Ayala, Joyce Woodhouse, Anastasya Shilova, et al. “Slow Conformational Exchange and Overall Rocking Motion in Ubiquitin Protein Crystals.” <i>Nature Communications</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>.","apa":"Kurauskas, V., Izmailov, S. A., Rogacheva, O. N., Hessel, A., Ayala, I., Woodhouse, J., … Schanda, P. (2017). Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-017-00165-8\">https://doi.org/10.1038/s41467-017-00165-8</a>","ama":"Kurauskas V, Izmailov SA, Rogacheva ON, et al. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/s41467-017-00165-8\">10.1038/s41467-017-00165-8</a>","short":"V. Kurauskas, S.A. Izmailov, O.N. Rogacheva, A. Hessel, I. Ayala, J. Woodhouse, A. Shilova, Y. Xue, T. Yuwen, N. Coquelle, J.-P. Colletier, N.R. Skrynnikov, P. Schanda, Nature Communications 8 (2017)."},"title":"Slow conformational exchange and overall rocking motion in ubiquitin protein crystals","day":"27","article_type":"original","oa_version":"Published Version","year":"2017","author":[{"first_name":"Vilius","full_name":"Kurauskas, Vilius","last_name":"Kurauskas"},{"full_name":"Izmailov, Sergei A.","first_name":"Sergei A.","last_name":"Izmailov"},{"last_name":"Rogacheva","first_name":"Olga N.","full_name":"Rogacheva, Olga N."},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"full_name":"Ayala, Isabel","first_name":"Isabel","last_name":"Ayala"},{"last_name":"Woodhouse","first_name":"Joyce","full_name":"Woodhouse, Joyce"},{"last_name":"Shilova","full_name":"Shilova, Anastasya","first_name":"Anastasya"},{"first_name":"Yi","full_name":"Xue, Yi","last_name":"Xue"},{"last_name":"Yuwen","first_name":"Tairan","full_name":"Yuwen, Tairan"},{"last_name":"Coquelle","first_name":"Nicolas","full_name":"Coquelle, Nicolas"},{"full_name":"Colletier, Jacques-Philippe","first_name":"Jacques-Philippe","last_name":"Colletier"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"type":"journal_article","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:19Z","doi":"10.1038/s41467-017-00165-8","publication_identifier":{"issn":["2041-1723"]}},{"doi":"10.1002/cphc.201700572","publication_identifier":{"issn":["1439-4235","1439-7641"]},"date_updated":"2021-01-12T08:19:19Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"oa_version":"None","year":"2017","type":"journal_article","author":[{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"last_name":"Arnaud","full_name":"Arnaud, Charles‐Adrien","first_name":"Charles‐Adrien"},{"full_name":"Gauto, Diego F.","first_name":"Diego F.","last_name":"Gauto"},{"first_name":"Maxime","full_name":"Audin, Maxime","last_name":"Audin"},{"last_name":"Kurauskas","first_name":"Vilius","full_name":"Kurauskas, Vilius"},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"first_name":"Carsten","full_name":"Krichel, Carsten","last_name":"Krichel"},{"full_name":"Guan, Jia‐Ying","first_name":"Jia‐Ying","last_name":"Guan"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome","first_name":"Jerome"},{"last_name":"Sprangers","full_name":"Sprangers, Remco","first_name":"Remco"},{"last_name":"Breyton","full_name":"Breyton, Cécile","first_name":"Cécile"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul"}],"day":"09","article_type":"original","title":"Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins","citation":{"mla":"Fraga, Hugo, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>, vol. 18, no. 19, Wiley, 2017, pp. 2697–703, doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>.","ieee":"H. Fraga <i>et al.</i>, “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins,” <i>ChemPhysChem</i>, vol. 18, no. 19. Wiley, pp. 2697–2703, 2017.","ista":"Fraga H, Arnaud C, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan J, Boisbouvier J, Sprangers R, Breyton C, Schanda P. 2017. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. ChemPhysChem. 18(19), 2697–2703.","chicago":"Fraga, Hugo, Charles‐Adrien Arnaud, Diego F. Gauto, Maxime Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, et al. “Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins.” <i>ChemPhysChem</i>. Wiley, 2017. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>.","apa":"Fraga, H., Arnaud, C., Gauto, D. F., Audin, M., Kurauskas, V., Macek, P., … Schanda, P. (2017). Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201700572\">https://doi.org/10.1002/cphc.201700572</a>","ama":"Fraga H, Arnaud C, Gauto DF, et al. Solid‐state NMR H–N–(C)–H and H–N–C–C 3D/4D correlation experiments for resonance assignment of large proteins. <i>ChemPhysChem</i>. 2017;18(19):2697-2703. doi:<a href=\"https://doi.org/10.1002/cphc.201700572\">10.1002/cphc.201700572</a>","short":"H. Fraga, C. Arnaud, D.F. Gauto, M. Audin, V. Kurauskas, P. Macek, C. Krichel, J. Guan, J. Boisbouvier, R. Sprangers, C. Breyton, P. Schanda, ChemPhysChem 18 (2017) 2697–2703."},"volume":18,"intvolume":"        18","status":"public","quality_controlled":"1","publication":"ChemPhysChem","publication_status":"published","publisher":"Wiley","_id":"8446","abstract":[{"lang":"eng","text":"Solid‐state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid‐state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1H‐detected assignment approaches, which correlate a given amide pair either to the two adjacent CO–CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross‐polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide‐protonated proteins from approximately 20 to 60 kDa monomer, at magic‐angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly."}],"date_created":"2020-09-18T10:06:09Z","date_published":"2017-08-09T00:00:00Z","extern":"1","month":"08","issue":"19","article_processing_charge":"No","page":"2697-2703"},{"publication_status":"published","publisher":"Elsevier","quality_controlled":"1","publication":"Solid State Nuclear Magnetic Resonance","volume":87,"status":"public","intvolume":"        87","page":"86-95","issue":"10","article_processing_charge":"No","extern":"1","month":"10","_id":"8447","abstract":[{"lang":"eng","text":"Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45–60 kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility."}],"date_published":"2017-10-01T00:00:00Z","date_created":"2020-09-18T10:06:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:20Z","language":[{"iso":"eng"}],"keyword":["Nuclear and High Energy Physics","Instrumentation","General Chemistry","Radiation"],"doi":"10.1016/j.ssnmr.2017.04.002","publication_identifier":{"issn":["0926-2040"]},"citation":{"mla":"Gauto, Diego F., et al. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10, Elsevier, 2017, pp. 86–95, doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>.","ista":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. 2017. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. Solid State Nuclear Magnetic Resonance. 87(10), 86–95.","ieee":"D. F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, and P. Schanda, “Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals,” <i>Solid State Nuclear Magnetic Resonance</i>, vol. 87, no. 10. Elsevier, pp. 86–95, 2017.","chicago":"Gauto, Diego F., Audrey Hessel, Petra Rovó, Vilius Kurauskas, Rasmus Linser, and Paul Schanda. “Protein Conformational Dynamics Studied by 15N and 1HR1ρ Relaxation Dispersion: Application to Wild-Type and G53A Ubiquitin Crystals.” <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>.","apa":"Gauto, D. F., Hessel, A., Rovó, P., Kurauskas, V., Linser, R., &#38; Schanda, P. (2017). Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">https://doi.org/10.1016/j.ssnmr.2017.04.002</a>","ama":"Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. <i>Solid State Nuclear Magnetic Resonance</i>. 2017;87(10):86-95. doi:<a href=\"https://doi.org/10.1016/j.ssnmr.2017.04.002\">10.1016/j.ssnmr.2017.04.002</a>","short":"D.F. Gauto, A. Hessel, P. Rovó, V. Kurauskas, R. Linser, P. Schanda, Solid State Nuclear Magnetic Resonance 87 (2017) 86–95."},"title":"Protein conformational dynamics studied by 15N and 1HR1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals","day":"01","article_type":"original","year":"2017","oa_version":"None","author":[{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"full_name":"Hessel, Audrey","first_name":"Audrey","last_name":"Hessel"},{"full_name":"Rovó, Petra","first_name":"Petra","last_name":"Rovó"},{"first_name":"Vilius","full_name":"Kurauskas, Vilius","last_name":"Kurauskas"},{"last_name":"Linser","full_name":"Linser, Rasmus","first_name":"Rasmus"},{"first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"type":"journal_article"},{"month":"08","extern":"1","date_created":"2020-09-18T10:06:27Z","_id":"8448","date_published":"2017-08-01T00:00:00Z","abstract":[{"text":"We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates.","lang":"eng"}],"page":"125-129","article_processing_charge":"No","issue":"8","publication":"Journal of Magnetic Resonance","quality_controlled":"1","status":"public","intvolume":"       281","volume":281,"publication_status":"published","publisher":"Elsevier","article_type":"original","day":"01","type":"journal_article","author":[{"full_name":"Franco, Rémi","first_name":"Rémi","last_name":"Franco"},{"last_name":"Favier","full_name":"Favier, Adrien","first_name":"Adrien"},{"first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"oa_version":"None","year":"2017","citation":{"apa":"Franco, R., Favier, A., Schanda, P., &#38; Brutscher, B. (2017). Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>","ama":"Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. 2017;281(8):125-129. doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>","short":"R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129.","mla":"Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8, Elsevier, 2017, pp. 125–29, doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>.","ieee":"R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing device for real-time NMR applications,” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8. Elsevier, pp. 125–129, 2017.","ista":"Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129.","chicago":"Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>."},"title":"Optimized fast mixing device for real-time NMR applications","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:20Z","publication_identifier":{"issn":["1090-7807"]},"doi":"10.1016/j.jmr.2017.05.016"},{"doi":"10.1093/nar/gkx044","publication_identifier":{"issn":["0305-1048","1362-4962"]},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:19:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","year":"2017","type":"journal_article","author":[{"last_name":"Rennella","full_name":"Rennella, Enrico","first_name":"Enrico"},{"first_name":"Tomáš","full_name":"Sára, Tomáš","last_name":"Sára"},{"full_name":"Juen, Michael","first_name":"Michael","last_name":"Juen"},{"last_name":"Wunderlich","full_name":"Wunderlich, Christoph","first_name":"Christoph"},{"last_name":"Imbert","full_name":"Imbert, Lionel","first_name":"Lionel"},{"first_name":"Zsofia","full_name":"Solyom, Zsofia","last_name":"Solyom"},{"last_name":"Favier","first_name":"Adrien","full_name":"Favier, Adrien"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina","first_name":"Katharina"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","last_name":"Schanda"},{"last_name":"Konrat","full_name":"Konrat, Robert","first_name":"Robert"},{"first_name":"Christoph","full_name":"Kreutz, Christoph","last_name":"Kreutz"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"day":"20","article_type":"original","title":"RNA binding and chaperone activity of the E.coli cold-shock protein CspA","citation":{"short":"E. Rennella, T. Sára, M. Juen, C. Wunderlich, L. Imbert, Z. Solyom, A. Favier, I. Ayala, K. Weinhäupl, P. Schanda, R. Konrat, C. Kreutz, B. Brutscher, Nucleic Acids Research 45 (2017) 4255–4268.","ama":"Rennella E, Sára T, Juen M, et al. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. 2017;45(7):4255-4268. doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>","apa":"Rennella, E., Sára, T., Juen, M., Wunderlich, C., Imbert, L., Solyom, Z., … Brutscher, B. (2017). RNA binding and chaperone activity of the E.coli cold-shock protein CspA. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>","chicago":"Rennella, Enrico, Tomáš Sára, Michael Juen, Christoph Wunderlich, Lionel Imbert, Zsofia Solyom, Adrien Favier, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/nar/gkx044\">https://doi.org/10.1093/nar/gkx044</a>.","ieee":"E. Rennella <i>et al.</i>, “RNA binding and chaperone activity of the E.coli cold-shock protein CspA,” <i>Nucleic Acids Research</i>, vol. 45, no. 7. Oxford University Press, pp. 4255–4268, 2017.","ista":"Rennella E, Sára T, Juen M, Wunderlich C, Imbert L, Solyom Z, Favier A, Ayala I, Weinhäupl K, Schanda P, Konrat R, Kreutz C, Brutscher B. 2017. RNA binding and chaperone activity of the E.coli cold-shock protein CspA. Nucleic Acids Research. 45(7), 4255–4268.","mla":"Rennella, Enrico, et al. “RNA Binding and Chaperone Activity of the E.Coli Cold-Shock Protein CspA.” <i>Nucleic Acids Research</i>, vol. 45, no. 7, Oxford University Press, 2017, pp. 4255–68, doi:<a href=\"https://doi.org/10.1093/nar/gkx044\">10.1093/nar/gkx044</a>."},"volume":45,"intvolume":"        45","status":"public","quality_controlled":"1","publication":"Nucleic Acids Research","publisher":"Oxford University Press","publication_status":"published","date_published":"2017-04-20T00:00:00Z","_id":"8449","abstract":[{"lang":"eng","text":"Ensuring the correct folding of RNA molecules in the cell is of major importance for a large variety of biological functions. Therefore, chaperone proteins that assist RNA in adopting their functionally active states are abundant in all living organisms. An important feature of RNA chaperone proteins is that they do not require an external energy source to perform their activity, and that they interact transiently and non-specifically with their RNA targets. So far, little is known about the mechanistic details of the RNA chaperone activity of these proteins. Prominent examples of RNA chaperones are bacterial cold shock proteins (Csp) that have been reported to bind single-stranded RNA and DNA. Here, we have used advanced NMR spectroscopy techniques to investigate at atomic resolution the RNA-melting activity of CspA, the major cold shock protein of Escherichia coli, upon binding to different RNA hairpins. Real-time NMR provides detailed information on the folding kinetics and folding pathways. Finally, comparison of wild-type CspA with single-point mutants and small peptides yields insights into the complementary roles of aromatic and positively charged amino-acid side chains for the RNA chaperone activity of the protein."}],"date_created":"2020-09-18T10:06:34Z","extern":"1","month":"04","issue":"7","article_processing_charge":"No","page":"4255-4268"}]