[{"publication":"2022 IEEE International Symposium on Information Theory","volume":2022,"title":"Lower bounds for multiple packing","_id":"12015","publisher":"IEEE","day":"03","date_published":"2022-08-03T00:00:00Z","year":"2022","intvolume":"      2022","abstract":[{"lang":"eng","text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let P, N > 0 and L∈Z≥2. A multiple packing is a set C of points in Bn(0–,nP−−−√) such that any point in ℝ n lies in the intersection of at most L – 1 balls of radius nN−−−√ around points in C. 1 In this paper, we derive two lower bounds on the largest possible density of a multiple packing. These bounds are obtained through a stronger notion called average-radius multiple packing. Specifically, we exactly pin down the asymptotics of (expurgated) Gaussian codes and (expurgated) spherical codes under average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. The bound for spherical codes matches the previous best known bound which was obtained for the standard (weaker) notion of multiple packing through a curious connection with error exponents [Bli99], [ZV21]. The bound for Gaussian codes suggests that they are strictly inferior to spherical codes."}],"date_created":"2022-09-04T22:02:05Z","quality_controlled":"1","page":"3085-3090","external_id":{"isi":["001254261903042"]},"publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"location":"Espoo, Finland","start_date":"2022-06-26","name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01"},"scopus_import":"1","citation":{"mla":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 3085–90, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">10.1109/ISIT50566.2022.9834443</a>.","ista":"Zhang Y, Vatedka S. 2022. Lower bounds for multiple packing. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 3085–3090.","ieee":"Y. Zhang and S. Vatedka, “Lower bounds for multiple packing,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 3085–3090.","short":"Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 3085–3090.","ama":"Zhang Y, Vatedka S. Lower bounds for multiple packing. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:3085-3090. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">10.1109/ISIT50566.2022.9834443</a>","chicago":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds for Multiple Packing.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:3085–90. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">https://doi.org/10.1109/ISIT50566.2022.9834443</a>.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). Lower bounds for multiple packing. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 3085–3090). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834443\">https://doi.org/10.1109/ISIT50566.2022.9834443</a>"},"language":[{"iso":"eng"}],"date_updated":"2025-09-10T09:44:24Z","department":[{"_id":"MaMo"}],"author":[{"full_name":"Zhang, Yihan","last_name":"Zhang","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258"},{"first_name":"Shashank","full_name":"Vatedka, Shashank","last_name":"Vatedka"}],"article_processing_charge":"No","publication_status":"published","doi":"10.1109/ISIT50566.2022.9834443","type":"conference","oa_version":"None","isi":1,"status":"public"},{"_id":"12016","publisher":"IEEE","arxiv":1,"day":"03","publication":"2022 IEEE International Symposium on Information Theory","volume":2022,"title":"Polar coded computing: The role of the scaling exponent","abstract":[{"lang":"eng","text":"We consider the problem of coded distributed computing using polar codes. The average execution time of a coded computing system is related to the error probability for transmission over the binary erasure channel in recent work by Soleymani, Jamali and Mahdavifar, where the performance of binary linear codes is investigated. In this paper, we focus on polar codes and unveil a connection between the average execution time and the scaling exponent μ of the family of codes. In the finite-length characterization of polar codes, the scaling exponent is a key object capturing the speed of convergence to capacity. In particular, we show that (i) the gap between the normalized average execution time of polar codes and that of optimal MDS codes is O(n –1/μ ), and (ii) this upper bound can be improved to roughly O(n –1/2 ) by considering polar codes with large kernels. We conjecture that these bounds could be improved to O(n –2/μ ) and O(n –1 ), respectively, and provide a heuristic argument as well as numerical evidence supporting this view."}],"date_created":"2022-09-04T22:02:05Z","intvolume":"      2022","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10082","open_access":"1"}],"quality_controlled":"1","date_published":"2022-08-03T00:00:00Z","year":"2022","oa":1,"scopus_import":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"citation":{"short":"D. Fathollahi, M. Mondelli, in:, 2022 IEEE International Symposium on Information Theory, IEEE, 2022, pp. 2154–2159.","ieee":"D. Fathollahi and M. Mondelli, “Polar coded computing: The role of the scaling exponent,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2154–2159.","ista":"Fathollahi D, Mondelli M. 2022. Polar coded computing: The role of the scaling exponent. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2154–2159.","mla":"Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role of the Scaling Exponent.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, IEEE, 2022, pp. 2154–59, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">10.1109/ISIT50566.2022.9834712</a>.","ama":"Fathollahi D, Mondelli M. Polar coded computing: The role of the scaling exponent. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. IEEE; 2022:2154-2159. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">10.1109/ISIT50566.2022.9834712</a>","apa":"Fathollahi, D., &#38; Mondelli, M. (2022). Polar coded computing: The role of the scaling exponent. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2154–2159). Espoo, Finland: IEEE. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">https://doi.org/10.1109/ISIT50566.2022.9834712</a>","chicago":"Fathollahi, Dorsa, and Marco Mondelli. “Polar Coded Computing: The Role of the Scaling Exponent.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2154–59. IEEE, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834712\">https://doi.org/10.1109/ISIT50566.2022.9834712</a>."},"language":[{"iso":"eng"}],"acknowledgement":"D. Fathollahi and M. Mondelli were partially supported by the 2019 Lopez-Loreta Prize. The authors thank Hamed Hassani and Hessam Mahdavifar for helpful discussions.","page":"2154-2159","external_id":{"arxiv":["2201.10082"],"isi":["001254261902052"]},"publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"end_date":"2022-07-01","name":"ISIT: International Symposium on Information Theory","location":"Espoo, Finland","start_date":"2022-06-26"},"publication_status":"published","doi":"10.1109/ISIT50566.2022.9834712","type":"conference","oa_version":"Preprint","isi":1,"status":"public","date_updated":"2025-09-10T09:43:32Z","department":[{"_id":"MaMo"}],"author":[{"first_name":"Dorsa","full_name":"Fathollahi, Dorsa","last_name":"Fathollahi"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli"}],"article_processing_charge":"No"},{"_id":"12017","publisher":"Institute of Electrical and Electronics Engineers","day":"03","volume":2022,"title":"New results on AVCs with omniscient and myopic adversaries","publication":"2022 IEEE International Symposium on Information Theory","intvolume":"      2022","date_created":"2022-09-04T22:02:06Z","abstract":[{"lang":"eng","text":"In the classic adversarial communication problem, two parties communicate over a noisy channel in the presence of a malicious jamming adversary. The arbitrarily varying channels (AVCs) offer an elegant framework to study a wide range of interesting adversary models. The optimal throughput or capacity over such AVCs is intimately tied to the underlying adversary model; in some cases, capacity is unknown and the problem is known to be notoriously hard. The omniscient adversary, one which knows the sender’s entire channel transmission a priori, is one of such classic models of interest; the capacity under such an adversary remains an exciting open problem. The myopic adversary is a generalization of that model where the adversary’s observation may be corrupted over a noisy discrete memoryless channel. Through the adversary’s myopicity, one can unify the slew of different adversary models, ranging from the omniscient adversary to one that is completely blind to the transmission (the latter is the well known oblivious model where the capacity is fully characterized).In this work, we present new results on the capacity under both the omniscient and myopic adversary models. We completely characterize the positive capacity threshold over general AVCs with omniscient adversaries. The characterization is in terms of two key combinatorial objects: the set of completely positive distributions and the CP-confusability set. For omniscient AVCs with positive capacity, we present non-trivial lower and upper bounds on the capacity; unlike some of the previous bounds, our bounds hold under fairly general input and jamming constraints. Our lower bound improves upon the generalized Gilbert-Varshamov bound for general AVCs while the upper bound generalizes the well known Elias-Bassalygo bound (known for binary and q-ary alphabets). For the myopic AVCs, we build on prior results known for the so-called sufficiently myopic model, and present new results on the positive rate communication threshold over the so-called insufficiently myopic regime (a completely insufficient myopic adversary specializes to an omniscient adversary). We present interesting examples for the widely studied models of adversarial bit-flip and bit-erasure channels. In fact, for the bit-flip AVC with additive adversarial noise as well as random noise, we completely characterize the omniscient model capacity when the random noise is sufficiently large vis-a-vis the adversary’s budget."}],"quality_controlled":"1","date_published":"2022-08-03T00:00:00Z","year":"2022","citation":{"apa":"Yadav, A. K., Alimohammadi, M., Zhang, Y., Budkuley, A. J., &#38; Jaggi, S. (2022). New results on AVCs with omniscient and myopic adversaries. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2535–2540). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">https://doi.org/10.1109/ISIT50566.2022.9834632</a>","chicago":"Yadav, Anuj Kumar, Mohammadreza Alimohammadi, Yihan Zhang, Amitalok J. Budkuley, and Sidharth Jaggi. “New Results on AVCs with Omniscient and Myopic Adversaries.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2535–40. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">https://doi.org/10.1109/ISIT50566.2022.9834632</a>.","ama":"Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. New results on AVCs with omniscient and myopic adversaries. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2535-2540. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">10.1109/ISIT50566.2022.9834632</a>","ieee":"A. K. Yadav, M. Alimohammadi, Y. Zhang, A. J. Budkuley, and S. Jaggi, “New results on AVCs with omniscient and myopic adversaries,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2535–2540.","short":"A.K. Yadav, M. Alimohammadi, Y. Zhang, A.J. Budkuley, S. Jaggi, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 2535–2540.","ista":"Yadav AK, Alimohammadi M, Zhang Y, Budkuley AJ, Jaggi S. 2022. New results on AVCs with omniscient and myopic adversaries. 2022 IEEE International Symposium on Information Theory. ISIT: Internation Symposium on Information Theory vol. 2022, 2535–2540.","mla":"Yadav, Anuj Kumar, et al. “New Results on AVCs with Omniscient and Myopic Adversaries.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2535–40, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834632\">10.1109/ISIT50566.2022.9834632</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"08","conference":{"name":"ISIT: Internation Symposium on Information Theory","location":"Espoo, Finland","start_date":"2022-06-26","end_date":"2022-07-01"},"page":"2535-2540","external_id":{"isi":["001254261902116"]},"publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"isi":1,"status":"public","publication_status":"published","doi":"10.1109/ISIT50566.2022.9834632","type":"conference","oa_version":"None","author":[{"first_name":"Anuj Kumar","last_name":"Yadav","full_name":"Yadav, Anuj Kumar"},{"first_name":"Mohammadreza","full_name":"Alimohammadi, Mohammadreza","last_name":"Alimohammadi"},{"first_name":"Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan"},{"last_name":"Budkuley","full_name":"Budkuley, Amitalok J.","first_name":"Amitalok J."},{"first_name":"Sidharth","full_name":"Jaggi, Sidharth","last_name":"Jaggi"}],"article_processing_charge":"No","date_updated":"2025-09-10T09:45:03Z","department":[{"_id":"MaMo"}]},{"citation":{"ista":"Zhang Y, Vatedka S. 2022. Lower bounds on list decoding capacity using error exponents. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 1324–1329.","ieee":"Y. Zhang and S. Vatedka, “Lower bounds on list decoding capacity using error exponents,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 1324–1329.","short":"Y. Zhang, S. Vatedka, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–1329.","mla":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity Using Error Exponents.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 1324–29, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">10.1109/ISIT50566.2022.9834815</a>.","ama":"Zhang Y, Vatedka S. Lower bounds on list decoding capacity using error exponents. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:1324-1329. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">10.1109/ISIT50566.2022.9834815</a>","apa":"Zhang, Y., &#38; Vatedka, S. (2022). Lower bounds on list decoding capacity using error exponents. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 1324–1329). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">https://doi.org/10.1109/ISIT50566.2022.9834815</a>","chicago":"Zhang, Yihan, and Shashank Vatedka. “Lower Bounds on List Decoding Capacity Using Error Exponents.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:1324–29. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834815\">https://doi.org/10.1109/ISIT50566.2022.9834815</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","conference":{"end_date":"2022-07-01","location":"Espoo, Finland","start_date":"2022-06-26","name":"ISIT: International Symposium on Information Theory"},"month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001254261901080"]},"page":"1324-1329","publication_identifier":{"issn":["2157-8095"],"isbn":["9781665421591"]},"isi":1,"status":"public","doi":"10.1109/ISIT50566.2022.9834815","publication_status":"published","oa_version":"None","type":"conference","article_processing_charge":"No","author":[{"last_name":"Zhang","full_name":"Zhang, Yihan","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"}],"date_updated":"2025-09-10T09:45:40Z","department":[{"_id":"MaMo"}],"_id":"12018","day":"03","publisher":"Institute of Electrical and Electronics Engineers","volume":2022,"title":"Lower bounds on list decoding capacity using error exponents","publication":"2022 IEEE International Symposium on Information Theory","date_created":"2022-09-04T22:02:06Z","intvolume":"      2022","abstract":[{"lang":"eng","text":"We study the problem of characterizing the maximal rates of list decoding in Euclidean spaces for finite list sizes. For any positive integer L ≥ 2 and real N > 0, we say that a subset C⊂Rn is an (N,L – 1)-multiple packing or an (N,L– 1)-list decodable code if every Euclidean ball of radius nN−−−√ in ℝ n contains no more than L − 1 points of C. We study this problem with and without ℓ 2 norm constraints on C, and derive the best-known lower bounds on the maximal rate for (N,L−1) multiple packing. Our bounds are obtained via error exponents for list decoding over Additive White Gaussian Noise (AWGN) channels. We establish a curious inequality which relates the error exponent, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We derive various bounds on the error exponent for list decoding in both bounded and unbounded settings which could be of independent interest beyond multiple packing."}],"quality_controlled":"1","date_published":"2022-08-03T00:00:00Z","year":"2022"},{"publication":"2022 IEEE International Symposium on Information Theory","volume":2022,"title":"List-decodable zero-rate codes for the Z-channel","_id":"12019","day":"03","publisher":"Institute of Electrical and Electronics Engineers","date_published":"2022-08-03T00:00:00Z","year":"2022","abstract":[{"lang":"eng","text":"This paper studies combinatorial properties of codes for the Z-channel. A Z-channel with error fraction τ takes as input a length-n binary codeword and injects in an adversarial manner up to nτ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest (L − 1)-list-decodable code for the Z-channel with error fraction τ has exponential (in n) size if τ is less than a critical value that we call the Plotkin point and has constant size if τ is larger than the threshold. The (L−1)-list-decoding Plotkin point is known to be L−1L−1−L−LL−1. In this paper, we show that the largest (L−1)-list-decodable code ε-above the Plotkin point has size Θ L (ε −3/2 ) for any L − 1 ≥ 1."}],"intvolume":"      2022","date_created":"2022-09-04T22:02:07Z","quality_controlled":"1","external_id":{"isi":["001254261902119"]},"page":"2553-2558","publication_identifier":{"isbn":["9781665421591"],"issn":["2157-8095"]},"conference":{"location":"Espoo, Finland","start_date":"2022-06-26","name":"ISIT: International Symposium on Information Theory","end_date":"2022-07-01"},"month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","citation":{"chicago":"Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for the Z-Channel.” In <i>2022 IEEE International Symposium on Information Theory</i>, 2022:2553–58. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">https://doi.org/10.1109/ISIT50566.2022.9834829</a>.","apa":"Polyanskii, N., &#38; Zhang, Y. (2022). List-decodable zero-rate codes for the Z-channel. In <i>2022 IEEE International Symposium on Information Theory</i> (Vol. 2022, pp. 2553–2558). Espoo, Finland: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">https://doi.org/10.1109/ISIT50566.2022.9834829</a>","ama":"Polyanskii N, Zhang Y. List-decodable zero-rate codes for the Z-channel. In: <i>2022 IEEE International Symposium on Information Theory</i>. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2553-2558. doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">10.1109/ISIT50566.2022.9834829</a>","mla":"Polyanskii, Nikita, and Yihan Zhang. “List-Decodable Zero-Rate Codes for the Z-Channel.” <i>2022 IEEE International Symposium on Information Theory</i>, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–58, doi:<a href=\"https://doi.org/10.1109/ISIT50566.2022.9834829\">10.1109/ISIT50566.2022.9834829</a>.","ieee":"N. Polyanskii and Y. Zhang, “List-decodable zero-rate codes for the Z-channel,” in <i>2022 IEEE International Symposium on Information Theory</i>, Espoo, Finland, 2022, vol. 2022, pp. 2553–2558.","ista":"Polyanskii N, Zhang Y. 2022. List-decodable zero-rate codes for the Z-channel. 2022 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory vol. 2022, 2553–2558.","short":"N. Polyanskii, Y. Zhang, in:, 2022 IEEE International Symposium on Information Theory, Institute of Electrical and Electronics Engineers, 2022, pp. 2553–2558."},"language":[{"iso":"eng"}],"date_updated":"2025-09-10T09:46:15Z","department":[{"_id":"MaMo"}],"author":[{"first_name":"Nikita","last_name":"Polyanskii","full_name":"Polyanskii, Nikita"},{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang"}],"article_processing_charge":"No","doi":"10.1109/ISIT50566.2022.9834829","publication_status":"published","oa_version":"None","type":"conference","isi":1,"status":"public"},{"article_type":"original","title":"The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans","volume":5,"publication":"Life Science Alliance","keyword":["Health","Toxicology and Mutagenesis","Plant Science","Biochemistry","Genetics and Molecular Biology (miscellaneous)","Ecology"],"ddc":["570"],"publisher":"Life Science Alliance","day":"01","_id":"12051","oa":1,"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)"},"year":"2022","issue":"11","date_published":"2022-09-01T00:00:00Z","quality_controlled":"1","date_created":"2022-09-06T18:45:23Z","abstract":[{"lang":"eng","text":"Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble."}],"intvolume":"         5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","publication_identifier":{"issn":["2575-1077"]},"file":[{"checksum":"4201d876a3e5e8b65e319d03300014ad","relation":"main_file","file_size":3183129,"file_name":"2022_LifeScienceAlliance_Daiss.pdf","date_updated":"2022-09-08T06:41:14Z","content_type":"application/pdf","creator":"dernst","file_id":"12062","date_created":"2022-09-08T06:41:14Z","access_level":"open_access","success":1}],"acknowledgement":"The authors especially thank Philip Gunkel for his contribution. We thank all\r\npast and present members of the Engel lab, Achim Griesenbeck, Colyn Crane-\r\nRobinson, Christophe Lotz, Marlene Vayssieres, Klaus Grasser, Herbert Tschochner, and Philipp Milkereit for help and discussion; Gerhard Lehmann and Nobert Eichner for IT support; Joost Zomerdijk for UBF-constructs, Volker Cordes for the Hela P2 cell line; Remco Sprangers for shared cell culture; Dina Grohmann and the Archaea Center for fermentation; and Thomas\r\nDresselhaus for access to fluorescence microscopes. This work was in part supported by the Emmy-Noether Programm (DFG grant no. EN 1204/1-1 to C Engel) of the German Research Council and Collaborative Research Center 960 (TP-A8 to C Engel).","external_id":{"isi":["000972702600001"]},"language":[{"iso":"eng"}],"citation":{"apa":"Daiß, J. L., Pilsl, M., Straub, K., Bleckmann, A., Höcherl, M., Heiss, F. B., … Engel, C. (2022). The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>","chicago":"Daiß, Julia L, Michael Pilsl, Kristina Straub, Andrea Bleckmann, Mona Höcherl, Florian B Heiss, Guillermo Abascal-Palacios, et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>. Life Science Alliance, 2022. <a href=\"https://doi.org/10.26508/lsa.202201568\">https://doi.org/10.26508/lsa.202201568</a>.","ama":"Daiß JL, Pilsl M, Straub K, et al. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. <i>Life Science Alliance</i>. 2022;5(11). doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>","ista":"Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tluckova K, Mars J-C, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. 2022. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Science Alliance. 5(11), e202201568.","ieee":"J. L. Daiß <i>et al.</i>, “The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans,” <i>Life Science Alliance</i>, vol. 5, no. 11. Life Science Alliance, 2022.","short":"J.L. Daiß, M. Pilsl, K. Straub, A. Bleckmann, M. Höcherl, F.B. Heiss, G. Abascal-Palacios, E.P. Ramsay, K. Tluckova, J.-C. Mars, T. Fürtges, A. Bruckmann, T. Rudack, C. Bernecky, V. Lamour, K. Panov, A. Vannini, T. Moss, C. Engel, Life Science Alliance 5 (2022).","mla":"Daiß, Julia L., et al. “The Human RNA Polymerase I Structure Reveals an HMG-like Docking Domain Specific to Metazoans.” <i>Life Science Alliance</i>, vol. 5, no. 11, e202201568, Life Science Alliance, 2022, doi:<a href=\"https://doi.org/10.26508/lsa.202201568\">10.26508/lsa.202201568</a>."},"article_number":"e202201568","has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2022-09-08T06:41:14Z","scopus_import":"1","author":[{"last_name":"Daiß","full_name":"Daiß, Julia L","first_name":"Julia L"},{"last_name":"Pilsl","full_name":"Pilsl, Michael","first_name":"Michael"},{"last_name":"Straub","full_name":"Straub, Kristina","first_name":"Kristina"},{"first_name":"Andrea","full_name":"Bleckmann, Andrea","last_name":"Bleckmann"},{"first_name":"Mona","full_name":"Höcherl, Mona","last_name":"Höcherl"},{"first_name":"Florian B","full_name":"Heiss, Florian B","last_name":"Heiss"},{"full_name":"Abascal-Palacios, Guillermo","last_name":"Abascal-Palacios","first_name":"Guillermo"},{"last_name":"Ramsay","full_name":"Ramsay, Ewan P","first_name":"Ewan P"},{"full_name":"Tluckova, Katarina","last_name":"Tluckova","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"first_name":"Jean-Clement","last_name":"Mars","full_name":"Mars, Jean-Clement"},{"last_name":"Fürtges","full_name":"Fürtges, Torben","first_name":"Torben"},{"full_name":"Bruckmann, Astrid","last_name":"Bruckmann","first_name":"Astrid"},{"first_name":"Till","last_name":"Rudack","full_name":"Rudack, Till"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky"},{"first_name":"Valérie","full_name":"Lamour, Valérie","last_name":"Lamour"},{"first_name":"Konstantin","last_name":"Panov","full_name":"Panov, Konstantin"},{"first_name":"Alessandro","last_name":"Vannini","full_name":"Vannini, Alessandro"},{"full_name":"Moss, Tom","last_name":"Moss","first_name":"Tom"},{"first_name":"Christoph","last_name":"Engel","full_name":"Engel, Christoph"}],"article_processing_charge":"No","department":[{"_id":"CaBe"}],"date_updated":"2024-10-21T06:01:48Z","status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.26508/lsa.202201568"},{"language":[{"iso":"eng"}],"citation":{"apa":"Konstantinova, N., Hörmayer, L., Glanc, M., Keshkeih, R., Tan, S., Di Donato, M., … Luschnig, C. (2022). WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>","chicago":"Konstantinova, N, Lukas Hörmayer, Matous Glanc, R Keshkeih, Shutang Tan, M Di Donato, K Retzer, et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-32888-8\">https://doi.org/10.1038/s41467-022-32888-8</a>.","ama":"Konstantinova N, Hörmayer L, Glanc M, et al. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>","ieee":"N. Konstantinova <i>et al.</i>, “WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","short":"N. Konstantinova, L. Hörmayer, M. Glanc, R. Keshkeih, S. Tan, M. Di Donato, K. Retzer, J. Moulinier-Anzola, M. Schwihla, B. Korbei, M. Geisler, J. Friml, C. Luschnig, Nature Communications 13 (2022).","ista":"Konstantinova N, Hörmayer L, Glanc M, Keshkeih R, Tan S, Di Donato M, Retzer K, Moulinier-Anzola J, Schwihla M, Korbei B, Geisler M, Friml J, Luschnig C. 2022. WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions. Nature Communications. 13, 5147.","mla":"Konstantinova, N., et al. “WAVY GROWTH Arabidopsis E3 Ubiquitin Ligases Affect Apical PIN Sorting Decisions.” <i>Nature Communications</i>, vol. 13, 5147, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-32888-8\">10.1038/s41467-022-32888-8</a>."},"has_accepted_license":"1","article_number":"5147","file_date_updated":"2022-09-08T07:46:16Z","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"scopus_import":"1","month":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2041-1723"]},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-33198-9"}]},"file":[{"file_id":"12063","date_created":"2022-09-08T07:46:16Z","success":1,"access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_name":"2022_NatureCommunications_Konstantinova.pdf","date_updated":"2022-09-08T07:46:16Z","checksum":"43336758c89cd6c045839089af070afe","relation":"main_file","file_size":6678579}],"acknowledgement":"We would like to thank Tatsuo Sakai, Marcus Heisler, Toru Fujiwara, Lucia Strader, Christian Hardtke, Malcolm Bennett, Claus Schwechheimer, Gerd Jürgens and Remko Offringa for sharing published materials and Alba Grau Gimeno for support. We are greatly indebted to Bert de Rybel for supporting N.K. and M.G. to work on the final stages of manuscript preparation as postdocs in his laboratory. A full-length SOR1 cDNA clone (J090099M14) was obtained from the National Agriculture and Food Research Organization (NARO, Japan). Support by the Multiscale Imaging Core Facility at the BOKU is greatly acknowledged. This work has been supported by grants from the Austrian Science Fund (FWF P25931-B16; P31493-B25 to Christian Luschnig; I3630-B25 to Jiří Friml; P30850-B32 to Barbara Korbei) and from the Swiss National Funds (31003A-165877/1 to Markus Geisler) and the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement No 885979 to Matouš Glanc).","external_id":{"pmid":["36050482"],"isi":["000848744900004"]},"status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1038/s41467-022-32888-8","author":[{"first_name":"N","full_name":"Konstantinova, N","last_name":"Konstantinova"},{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous"},{"first_name":"R","full_name":"Keshkeih, R","last_name":"Keshkeih"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang"},{"last_name":"Di Donato","full_name":"Di Donato, M","first_name":"M"},{"first_name":"K","full_name":"Retzer, K","last_name":"Retzer"},{"first_name":"J","last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, J"},{"full_name":"Schwihla, M","last_name":"Schwihla","first_name":"M"},{"full_name":"Korbei, B","last_name":"Korbei","first_name":"B"},{"full_name":"Geisler, M","last_name":"Geisler","first_name":"M"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"full_name":"Luschnig, C","last_name":"Luschnig","first_name":"C"}],"article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_updated":"2025-04-15T07:32:09Z","pmid":1,"ddc":["580"],"publisher":"Springer Nature","day":"01","_id":"12052","article_type":"original","title":"WAVY GROWTH Arabidopsis E3 ubiquitin ligases affect apical PIN sorting decisions","volume":13,"publication":"Nature Communications","quality_controlled":"1","intvolume":"        13","date_created":"2022-09-07T14:19:26Z","abstract":[{"lang":"eng","text":"Directionality in the intercellular transport of the plant hormone auxin is determined by polar plasma membrane localization of PIN-FORMED (PIN) auxin transport proteins. However, apart from PIN phosphorylation at conserved motifs, no further determinants explicitly controlling polar PIN sorting decisions have been identified. Here we present Arabidopsis WAVY GROWTH 3 (WAV3) and closely related RING-finger E3 ubiquitin ligases, whose loss-of-function mutants show a striking apical-to-basal polarity switch in PIN2 localization in root meristem cells. WAV3 E3 ligases function as essential determinants for PIN polarity, acting independently from PINOID/WAG-dependent PIN phosphorylation. They antagonize ectopic deposition of de novo synthesized PIN proteins already immediately following completion of cell division, presumably via preventing PIN sorting into basal, ARF GEF-mediated trafficking. Our findings reveal an involvement of E3 ligases in the selective targeting of apically localized PINs in higher plants."}],"oa":1,"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)"},"year":"2022","date_published":"2022-09-01T00:00:00Z"},{"date_created":"2022-09-07T14:19:39Z","abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a class of phytohormones that regulate plant shoot branching and adventitious root development. However, little is known regarding the role of SLs in controlling the behavior of the smallest unit of the organism, the single cell. Here, taking advantage of a classic single-cell model offered by the cotton (Gossypium hirsutum) fiber cell, we show that SLs, whose biosynthesis is fine-tuned by gibberellins (GAs), positively regulate cell elongation and cell wall thickness by promoting the biosynthesis of very-long-chain fatty acids (VLCFAs) and cellulose, respectively. Furthermore, we identified two layers of transcription factors (TFs) involved in the hierarchical regulation of this GA-SL crosstalk. The top-layer TF GROWTH-REGULATING FACTOR 4 (GhGRF4) directly activates expression of the SL biosynthetic gene DWARF27 (D27) to increase SL accumulation in fiber cells and GAs induce GhGRF4 expression. SLs induce the expression of four second-layer TF genes (GhNAC100-2, GhBLH51, GhGT2, and GhB9SHZ1), which transmit SL signals downstream to two ketoacyl-CoA synthase genes (KCS) and three cellulose synthase (CesA) genes by directly activating their transcription. Finally, the KCS and CesA enzymes catalyze the biosynthesis of very long chain fatty acids and cellulose, respectively, to regulate development of high-grade cotton fibers. In addition to providing a theoretical basis for cotton fiber improvement, our results shed light on SL signaling in plant development at the single-cell level."}],"intvolume":"        34","quality_controlled":"1","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2022-12-01T00:00:00Z","year":"2022","issue":"12","ddc":["580"],"pmid":1,"_id":"12053","publisher":"Oxford University Press","day":"01","volume":34,"article_type":"original","title":"Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum)","publication":"The Plant Cell","isi":1,"status":"public","publication_status":"published","doi":"10.1093/plcell/koac270","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","author":[{"first_name":"Z","last_name":"Tian","full_name":"Tian, Z"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","first_name":"Yuzhou"},{"first_name":"L","full_name":"Zhu, L","last_name":"Zhu"},{"last_name":"Jiang","full_name":"Jiang, B","first_name":"B"},{"full_name":"Wang, H","last_name":"Wang","first_name":"H"},{"full_name":"Gao, R","last_name":"Gao","first_name":"R"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"G","last_name":"Xiao","full_name":"Xiao, G"}],"date_updated":"2025-04-15T08:12:07Z","department":[{"_id":"JiFr"}],"citation":{"ama":"Tian Z, Zhang Y, Zhu L, et al. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). <i>The Plant Cell</i>. 2022;34(12):4816-4839. doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>","apa":"Tian, Z., Zhang, Y., Zhu, L., Jiang, B., Wang, H., Gao, R., … Xiao, G. (2022). Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>","chicago":"Tian, Z, Yuzhou Zhang, L Zhu, B Jiang, H Wang, R Gao, Jiří Friml, and G Xiao. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <i>The Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac270\">https://doi.org/10.1093/plcell/koac270</a>.","ista":"Tian Z, Zhang Y, Zhu L, Jiang B, Wang H, Gao R, Friml J, Xiao G. 2022. Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum). The Plant Cell. 34(12), 4816–4839.","ieee":"Z. Tian <i>et al.</i>, “Strigolactones act downstream of gibberellins to regulate fiber cell elongation and cell wall thickness in cotton (Gossypium hirsutum),” <i>The Plant Cell</i>, vol. 34, no. 12. Oxford University Press, pp. 4816–4839, 2022.","short":"Z. Tian, Y. Zhang, L. Zhu, B. Jiang, H. Wang, R. Gao, J. Friml, G. Xiao, The Plant Cell 34 (2022) 4816–4839.","mla":"Tian, Z., et al. “Strigolactones Act Downstream of Gibberellins to Regulate Fiber Cell Elongation and Cell Wall Thickness in Cotton (Gossypium Hirsutum).” <i>The Plant Cell</i>, vol. 34, no. 12, Oxford University Press, 2022, pp. 4816–39, doi:<a href=\"https://doi.org/10.1093/plcell/koac270\">10.1093/plcell/koac270</a>."},"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2023-01-20T08:29:12Z","project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","file":[{"checksum":"1c606d9545f29dfca15235f69ad27b58","relation":"main_file","file_size":3282540,"file_name":"2022_PlantCell_Tian.pdf","date_updated":"2023-01-20T08:29:12Z","creator":"dernst","content_type":"application/pdf","file_id":"12318","date_created":"2023-01-20T08:29:12Z","success":1,"access_level":"open_access"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1093/plcell/koac342"}]},"acknowledgement":"This work was supported by the National Natural Science Foundation of China (32070549), Shaanxi Youth Entrusted Talent Program (20190205), Fundamental Research Funds for the Central Universities (GK202002005 and GK202201017), Young Elite Scientists Sponsorship Program by China Association for Science and Technology (CAST) (2019-2021QNRC001), State Key Laboratory of Cotton Biology Open Fund (CB2020A12 and CB2021A21) and FWF Stand-alone Project (P29988).","page":"4816-4839","external_id":{"pmid":["36040191"],"isi":["000852753000001"]},"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]}},{"status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.1038/s41586-022-05143-9","publication_status":"published","article_processing_charge":"No","author":[{"full_name":"Yang, Z","last_name":"Yang","first_name":"Z"},{"full_name":"Xia, J","last_name":"Xia","first_name":"J"},{"last_name":"Hong","full_name":"Hong, J","first_name":"J"},{"first_name":"C","last_name":"Zhang","full_name":"Zhang, C"},{"full_name":"Wei, H","last_name":"Wei","first_name":"H"},{"first_name":"W","last_name":"Ying","full_name":"Ying, W"},{"first_name":"C","full_name":"Sun, C","last_name":"Sun"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"},{"first_name":"Y","last_name":"Mao","full_name":"Mao, Y"},{"full_name":"Gao, Y","last_name":"Gao","first_name":"Y"},{"first_name":"S","last_name":"Tan","full_name":"Tan, S"},{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Li","full_name":"Li, D","first_name":"D"},{"full_name":"Liu, X","last_name":"Liu","first_name":"X"},{"first_name":"L","last_name":"Sun","full_name":"Sun, L"}],"department":[{"_id":"JiFr"}],"date_updated":"2023-08-03T13:41:44Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"apa":"Yang, Z., Xia, J., Hong, J., Zhang, C., Wei, H., Ying, W., … Sun, L. (2022). Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>","chicago":"Yang, Z, J Xia, J Hong, C Zhang, H Wei, W Ying, C Sun, et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05143-9\">https://doi.org/10.1038/s41586-022-05143-9</a>.","ama":"Yang Z, Xia J, Hong J, et al. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. <i>Nature</i>. 2022;609(7927):611-615. doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>","ieee":"Z. Yang <i>et al.</i>, “Structural insights into auxin recognition and efflux by Arabidopsis PIN1,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 611–615, 2022.","ista":"Yang Z, Xia J, Hong J, Zhang C, Wei H, Ying W, Sun C, Sun L, Mao Y, Gao Y, Tan S, Friml J, Li D, Liu X, Sun L. 2022. Structural insights into auxin recognition and efflux by Arabidopsis PIN1. Nature. 609(7927), 611–615.","short":"Z. Yang, J. Xia, J. Hong, C. Zhang, H. Wei, W. Ying, C. Sun, L. Sun, Y. Mao, Y. Gao, S. Tan, J. Friml, D. Li, X. Liu, L. Sun, Nature 609 (2022) 611–615.","mla":"Yang, Z., et al. “Structural Insights into Auxin Recognition and Efflux by Arabidopsis PIN1.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 611–15, doi:<a href=\"https://doi.org/10.1038/s41586-022-05143-9\">10.1038/s41586-022-05143-9</a>."},"file_date_updated":"2022-09-08T08:02:54Z","scopus_import":"1","month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"external_id":{"isi":["000848082900002"],"pmid":["35917925"]},"acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China (USTC) and the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science, for the EM facility support; we thank B. Zhu, X. Huang and all the other staff members for their technical support on cryo-EM data collection. We thank J. Ren for his technical support with the transport assays and M. Seeger for providing the sybody libraries. This work was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB 37020204 to D.L. and XDB37020103 to Linfeng Sun), National Natural Science Foundation of China (82151215 and 31870726 to D.L., 31900885 to X.L., and 31870732 to Linfeng Sun), Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun), the Fundamental Research Funds for the Central Universities (WK9100000031 to Linfeng Sun), and the USTC Research Funds of the Double First-Class Initiative (YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation, and a Young Scholar Award from the Cyrus Tang Foundation.","file":[{"file_name":"2022_Nature_Yang.pdf","date_updated":"2022-09-08T08:02:54Z","file_size":32344580,"checksum":"3136a585f8e1c7e73b5e1418b3d01898","relation":"main_file","date_created":"2022-09-08T08:02:54Z","success":1,"access_level":"open_access","file_id":"12064","content_type":"application/pdf","creator":"dernst"}],"page":"611-615","quality_controlled":"1","intvolume":"       609","date_created":"2022-09-07T14:19:52Z","abstract":[{"lang":"eng","text":"Polar auxin transport is unique to plants and coordinates their growth and development1,2. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport3,4; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold5. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development."}],"oa":1,"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)"},"issue":"7927","year":"2022","date_published":"2022-08-02T00:00:00Z","pmid":1,"ddc":["580"],"day":"02","publisher":"Springer Nature","_id":"12054","title":"Structural insights into auxin recognition and efflux by Arabidopsis PIN1","article_type":"original","volume":609,"publication":"Nature"},{"oa":1,"issue":"29","year":"2022","date_published":"2022-07-17T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv-2022-mstv5","open_access":"1"}],"intvolume":"        24","date_created":"2022-09-08T11:34:30Z","abstract":[{"lang":"eng","text":"We present a divergent strategy for the fluorination of phenylacetic acid derivatives that is induced by a charge-transfer complex between Selectfluor and 4-(dimethylamino)pyridine. A comprehensive investigation of the conditions revealed a critical role of the solvent on the reaction outcome. In the presence of water, decarboxylative fluorination through a single-electron oxidation is dominant. Non-aqueous conditions result in the clean formation of α-fluoro-α-arylcarboxylic acids."}],"article_type":"original","title":"Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch","volume":24,"publication":"Organic Letters","day":"17","publisher":"American Chemical Society","_id":"12067","author":[{"last_name":"Madani","full_name":"Madani, Amiera","first_name":"Amiera"},{"first_name":"Lucia","full_name":"Anghileri, Lucia","last_name":"Anghileri"},{"first_name":"Matthias","last_name":"Heydenreich","full_name":"Heydenreich, Matthias"},{"last_name":"Möller","full_name":"Möller, Heiko M.","first_name":"Heiko M."},{"orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus","full_name":"Pieber, Bartholomäus","last_name":"Pieber"}],"article_processing_charge":"No","date_updated":"2024-10-14T12:04:54Z","status":"public","oa_version":"Published Version","type":"journal_article","doi":"10.1021/acs.orglett.2c02050","publication_status":"published","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1523-7060"],"eissn":["1523-7052"]},"page":"5376–5380","language":[{"iso":"eng"}],"citation":{"chicago":"Madani, Amiera, Lucia Anghileri, Matthias Heydenreich, Heiko M. Möller, and Bartholomäus Pieber. “Benzylic Fluorination Induced by a Charge-Transfer Complex with a Solvent-Dependent Selectivity Switch.” <i>Organic Letters</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">https://doi.org/10.1021/acs.orglett.2c02050</a>.","apa":"Madani, A., Anghileri, L., Heydenreich, M., Möller, H. M., &#38; Pieber, B. (2022). Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. <i>Organic Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">https://doi.org/10.1021/acs.orglett.2c02050</a>","ama":"Madani A, Anghileri L, Heydenreich M, Möller HM, Pieber B. Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. <i>Organic Letters</i>. 2022;24(29):5376–5380. doi:<a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">10.1021/acs.orglett.2c02050</a>","mla":"Madani, Amiera, et al. “Benzylic Fluorination Induced by a Charge-Transfer Complex with a Solvent-Dependent Selectivity Switch.” <i>Organic Letters</i>, vol. 24, no. 29, American Chemical Society, 2022, pp. 5376–5380, doi:<a href=\"https://doi.org/10.1021/acs.orglett.2c02050\">10.1021/acs.orglett.2c02050</a>.","ieee":"A. Madani, L. Anghileri, M. Heydenreich, H. M. Möller, and B. Pieber, “Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch,” <i>Organic Letters</i>, vol. 24, no. 29. American Chemical Society, pp. 5376–5380, 2022.","short":"A. Madani, L. Anghileri, M. Heydenreich, H.M. Möller, B. Pieber, Organic Letters 24 (2022) 5376–5380.","ista":"Madani A, Anghileri L, Heydenreich M, Möller HM, Pieber B. 2022. Benzylic fluorination induced by a charge-transfer complex with a solvent-dependent selectivity switch. Organic Letters. 24(29), 5376–5380."},"scopus_import":"1","extern":"1"},{"date_published":"2022-08-24T00:00:00Z","year":"2022","issue":"6","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)"},"oa":1,"date_created":"2022-09-11T22:01:54Z","abstract":[{"text":"We extend the recent rigorous convergence result of Abels and Moser (SIAM J Math Anal 54(1):114–172, 2022. https://doi.org/10.1137/21M1424925) concerning convergence rates for solutions of the Allen–Cahn equation with a nonlinear Robin boundary condition towards evolution by mean curvature flow with constant contact angle. More precisely, in the present work we manage to remove the perturbative assumption on the contact angle being close to 90∘. We establish under usual double-well type assumptions on the potential and for a certain class of boundary energy densities the sub-optimal convergence rate of order ε12 for general contact angles α∈(0,π). For a very specific form of the boundary energy density, we even obtain from our methods a sharp convergence rate of order ε; again for general contact angles α∈(0,π). Our proof deviates from the popular strategy based on rigorous asymptotic expansions and stability estimates for the linearized Allen–Cahn operator. Instead, we follow the recent approach by Fischer et al. (SIAM J Math Anal 52(6):6222–6233, 2020. https://doi.org/10.1137/20M1322182), thus relying on a relative entropy technique. We develop a careful adaptation of their approach in order to encode the constant contact angle condition. In fact, we perform this task at the level of the notion of gradient flow calibrations. This concept was recently introduced in the context of weak-strong uniqueness for multiphase mean curvature flow by Fischer et al. (arXiv:2003.05478v2).","lang":"eng"}],"intvolume":"        61","quality_controlled":"1","publication":"Calculus of Variations and Partial Differential Equations","volume":61,"ec_funded":1,"article_type":"original","title":"Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime","_id":"12079","publisher":"Springer Nature","day":"24","ddc":["510"],"date_updated":"2025-04-14T07:53:59Z","department":[{"_id":"JuFi"}],"article_processing_charge":"No","author":[{"last_name":"Hensel","full_name":"Hensel, Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","first_name":"Sebastian"},{"last_name":"Moser","full_name":"Moser, Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian"}],"publication_status":"published","doi":"10.1007/s00526-022-02307-3","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"This Project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 948819)  , and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2047/1 - 390685813.\r\nOpen Access funding enabled and organized by Projekt DEAL.","file":[{"checksum":"b2da020ce50440080feedabeab5b09c4","relation":"main_file","file_size":1278493,"file_name":"2022_Calculus_Hensel.pdf","date_updated":"2023-01-20T08:56:01Z","creator":"dernst","content_type":"application/pdf","file_id":"12320","date_created":"2023-01-20T08:56:01Z","success":1,"access_level":"open_access"}],"external_id":{"isi":["000844247300008"]},"publication_identifier":{"issn":["0944-2669"],"eissn":["1432-0835"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","scopus_import":"1","file_date_updated":"2023-01-20T08:56:01Z","project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819"}],"citation":{"short":"S. Hensel, M. Moser, Calculus of Variations and Partial Differential Equations 61 (2022).","ieee":"S. Hensel and M. Moser, “Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 61, no. 6. Springer Nature, 2022.","ista":"Hensel S, Moser M. 2022. Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. Calculus of Variations and Partial Differential Equations. 61(6), 201.","mla":"Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn Equation with Boundary Contact Energy: The Non-Perturbative Regime.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 61, no. 6, 201, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s00526-022-02307-3\">10.1007/s00526-022-02307-3</a>.","ama":"Hensel S, Moser M. Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. <i>Calculus of Variations and Partial Differential Equations</i>. 2022;61(6). doi:<a href=\"https://doi.org/10.1007/s00526-022-02307-3\">10.1007/s00526-022-02307-3</a>","apa":"Hensel, S., &#38; Moser, M. (2022). Convergence rates for the Allen–Cahn equation with boundary contact energy: The non-perturbative regime. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-022-02307-3\">https://doi.org/10.1007/s00526-022-02307-3</a>","chicago":"Hensel, Sebastian, and Maximilian Moser. “Convergence Rates for the Allen–Cahn Equation with Boundary Contact Energy: The Non-Perturbative Regime.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00526-022-02307-3\">https://doi.org/10.1007/s00526-022-02307-3</a>."},"article_number":"201","has_accepted_license":"1","language":[{"iso":"eng"}]},{"pmid":1,"ddc":["570"],"publisher":"Elsevier","day":"01","_id":"12082","ec_funded":1,"title":"Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans","article_type":"original","volume":298,"publication":"Journal of Biological Chemistry","quality_controlled":"1","intvolume":"       298","date_created":"2022-09-11T22:01:55Z","abstract":[{"lang":"eng","text":"Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest."}],"oa":1,"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)"},"year":"2022","issue":"9","date_published":"2022-09-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Artan, Murat, Markus Hartl, Weiqiang Chen, and Mario de Bono. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>.","apa":"Artan, M., Hartl, M., Chen, W., &#38; de Bono, M. (2022). Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">https://doi.org/10.1016/j.jbc.2022.102343</a>","ama":"Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. <i>Journal of Biological Chemistry</i>. 2022;298(9). doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>","mla":"Artan, Murat, et al. “Depletion of Endogenously Biotinylated Carboxylases Enhances the Sensitivity of TurboID-Mediated Proximity Labeling in Caenorhabditis Elegans.” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9, 102343, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jbc.2022.102343\">10.1016/j.jbc.2022.102343</a>.","ista":"Artan M, Hartl M, Chen W, de Bono M. 2022. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. Journal of Biological Chemistry. 298(9), 102343.","ieee":"M. Artan, M. Hartl, W. Chen, and M. de Bono, “Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans,” <i>Journal of Biological Chemistry</i>, vol. 298, no. 9. Elsevier, 2022.","short":"M. Artan, M. Hartl, W. Chen, M. de Bono, Journal of Biological Chemistry 298 (2022)."},"article_number":"102343","has_accepted_license":"1","corr_author":"1","file_date_updated":"2022-09-12T08:14:50Z","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"file":[{"file_id":"12092","success":1,"access_level":"open_access","date_created":"2022-09-12T08:14:50Z","content_type":"application/pdf","creator":"dernst","file_name":"2022_JBC_Artan.pdf","date_updated":"2022-09-12T08:14:50Z","relation":"main_file","checksum":"e726c7b9315230e6710e0b1f1d1677e9","file_size":2101656}],"acknowledgement":"We thank de Bono laboratory members for helpful comments on the article and the Mass Spec Facilities at IST Austria and Max Perutz Labs for invaluable discussions and comments on how to optimize mass spec analyses of worm samples. We are grateful to Ekaterina Lashmanova for designing the degron knock-in constructs and preparing the injection mixes for CRISPR/Cas9-mediated genome editing. All LC–MS/MS analyses were performed on instruments of the Vienna BioCenter Core Facilities instrument pool.\r\nThis work was supported by a Wellcome Investigator Award (grant no.: 209504/Z/17/Z ) to M.d.B. and an ISTplus Fellowship to M.A. (Marie Sklodowska-Curie agreement no.: 754411).","acknowledged_ssus":[{"_id":"Bio"}],"external_id":{"pmid":["35933017"],"isi":["000884241800011"]},"status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1016/j.jbc.2022.102343","author":[{"full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","first_name":"Murat"},{"full_name":"Hartl, Markus","last_name":"Hartl","first_name":"Markus"},{"last_name":"Chen","full_name":"Chen, Weiqiang","first_name":"Weiqiang"},{"full_name":"De Bono, Mario","last_name":"De Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"MaDe"}],"date_updated":"2025-04-14T07:44:00Z"},{"article_number":"081902","has_accepted_license":"1","citation":{"ama":"Rademacher SAE. Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. 2022;63(8). doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>","apa":"Rademacher, S. A. E. (2022). Dependent random variables in quantum dynamics. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>","chicago":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0086712\">https://doi.org/10.1063/5.0086712</a>.","ista":"Rademacher SAE. 2022. Dependent random variables in quantum dynamics. Journal of Mathematical Physics. 63(8), 081902.","short":"S.A.E. Rademacher, Journal of Mathematical Physics 63 (2022).","ieee":"S. A. E. Rademacher, “Dependent random variables in quantum dynamics,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8. AIP Publishing, 2022.","mla":"Rademacher, Simone Anna Elvira. “Dependent Random Variables in Quantum Dynamics.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 8, 081902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0086712\">10.1063/5.0086712</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2022-09-12T07:35:34Z","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"corr_author":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","external_id":{"isi":["000844402500001"],"arxiv":["2112.04817"]},"acknowledgement":"S.R. would like to thank Robert Seiringer and Benedikt Stufler for helpful discussions. Funding from the European Union’s Horizon 2020 Research and Innovation Program under the ERC grant (Grant Agreement No. 694227) and under the Marie Skłodowska-Curie grant (Agreement No. 754411) is acknowledged.","file":[{"relation":"main_file","checksum":"e6fb0cf3f0327739c5e69a2cfc4020eb","file_size":4552261,"date_updated":"2022-09-12T07:35:34Z","file_name":"2022_JourMathPhysics_Rademacher.pdf","creator":"dernst","content_type":"application/pdf","file_id":"12089","success":1,"access_level":"open_access","date_created":"2022-09-12T07:35:34Z"}],"publication_identifier":{"issn":["0022-2488"]},"isi":1,"status":"public","doi":"10.1063/5.0086712","publication_status":"published","oa_version":"Published Version","type":"journal_article","article_processing_charge":"No","author":[{"full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"}],"date_updated":"2025-04-14T07:26:59Z","department":[{"_id":"RoSe"}],"ddc":["510"],"_id":"12083","day":"25","arxiv":1,"publisher":"AIP Publishing","volume":63,"title":"Dependent random variables in quantum dynamics","article_type":"original","ec_funded":1,"publication":"Journal of Mathematical Physics","abstract":[{"text":"We consider the many-body time evolution of weakly interacting bosons in the mean field regime for initial coherent states. We show that bounded k-particle operators, corresponding to dependent random variables, satisfy both a law of large numbers and a central limit theorem.","lang":"eng"}],"date_created":"2022-09-11T22:01:56Z","intvolume":"        63","quality_controlled":"1","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)"},"oa":1,"date_published":"2022-08-25T00:00:00Z","issue":"8","year":"2022"},{"date_published":"2022-08-15T00:00:00Z","year":"2022","issue":"8","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)"},"oa":1,"date_created":"2022-09-11T22:01:56Z","abstract":[{"text":"Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes.","lang":"eng"}],"intvolume":"        18","quality_controlled":"1","publication":"PLoS Computational Biology","volume":18,"article_type":"original","title":"Regimes and mechanisms of transient amplification in abstract and biological neural networks","_id":"12084","publisher":"Public Library of Science","day":"15","ddc":["570"],"pmid":1,"date_updated":"2025-06-11T13:51:21Z","department":[{"_id":"TiVo"}],"author":[{"first_name":"Georgia","last_name":"Christodoulou","full_name":"Christodoulou, Georgia"},{"full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181"},{"last_name":"Agnes","full_name":"Agnes, Everton J.","first_name":"Everton J."}],"article_processing_charge":"No","publication_status":"published","doi":"10.1371/journal.pcbi.1010365","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"12090","date_created":"2022-09-12T07:47:55Z","success":1,"access_level":"open_access","checksum":"8a81ab29f837991ee0ea770817c4a50e","relation":"main_file","file_size":2867337,"date_updated":"2022-09-12T07:47:55Z","file_name":"2022_PLoSCompBio_Christodoulou.pdf"}],"acknowledgement":"We thank Friedemann Zenke for his comments, especially on the effect of the self loops on the spectrum. We also thank Ken Miller and Bill Podlaski for helpful comments. This research was funded by a Wellcome Trust and Royal Society Henry Dale Research Fellowship (WT100000; TPV), a Wellcome Senior Research Fellowship (214316/Z/18/Z; GC, EJA, and TPV), and a Research Project Grant by the Leverhulme Trust (RPG-2016-446; EJA and TPV). ","external_id":{"isi":["000937227700001"],"pmid":["35969604"]},"publication_identifier":{"eissn":["1553-7358"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","scopus_import":"1","corr_author":"1","file_date_updated":"2022-09-12T07:47:55Z","project":[{"grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."}],"citation":{"ieee":"G. Christodoulou, T. P. Vogels, and E. J. Agnes, “Regimes and mechanisms of transient amplification in abstract and biological neural networks,” <i>PLoS Computational Biology</i>, vol. 18, no. 8. Public Library of Science, 2022.","short":"G. Christodoulou, T.P. Vogels, E.J. Agnes, PLoS Computational Biology 18 (2022).","ista":"Christodoulou G, Vogels TP, Agnes EJ. 2022. Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. 18(8), e1010365.","mla":"Christodoulou, Georgia, et al. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>, vol. 18, no. 8, e1010365, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>.","apa":"Christodoulou, G., Vogels, T. P., &#38; Agnes, E. J. (2022). Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>","chicago":"Christodoulou, Georgia, Tim P Vogels, and Everton J. Agnes. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” <i>PLoS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">https://doi.org/10.1371/journal.pcbi.1010365</a>.","ama":"Christodoulou G, Vogels TP, Agnes EJ. Regimes and mechanisms of transient amplification in abstract and biological neural networks. <i>PLoS Computational Biology</i>. 2022;18(8). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010365\">10.1371/journal.pcbi.1010365</a>"},"article_number":"e1010365","has_accepted_license":"1","language":[{"iso":"eng"}]},{"pmid":1,"_id":"12085","day":"01","publisher":"Springer Nature","volume":21,"title":"Weak catch bonds make strong networks","article_type":"original","publication":"Nature Materials","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.27.219618"}],"date_created":"2022-09-11T22:01:57Z","intvolume":"        21","abstract":[{"lang":"eng","text":"Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides ‘strength on demand3’, thus enabling cells to increase rigidity under stress1,4,5,6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This ‘dissociation on demand’ explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials."}],"quality_controlled":"1","oa":1,"date_published":"2022-09-01T00:00:00Z","issue":"9","year":"2022","citation":{"mla":"Mulla, Yuval, et al. “Weak Catch Bonds Make Strong Networks.” <i>Nature Materials</i>, vol. 21, no. 9, Springer Nature, 2022, pp. 1019–23, doi:<a href=\"https://doi.org/10.1038/s41563-022-01288-0\">10.1038/s41563-022-01288-0</a>.","ista":"Mulla Y, Avellaneda Sarrió M, Roland A, Baldauf L, Jung W, Kim T, Tans SJ, Koenderink GH. 2022. Weak catch bonds make strong networks. Nature Materials. 21(9), 1019–1023.","ieee":"Y. Mulla <i>et al.</i>, “Weak catch bonds make strong networks,” <i>Nature Materials</i>, vol. 21, no. 9. Springer Nature, pp. 1019–1023, 2022.","short":"Y. Mulla, M. Avellaneda Sarrió, A. Roland, L. Baldauf, W. Jung, T. Kim, S.J. Tans, G.H. Koenderink, Nature Materials 21 (2022) 1019–1023.","ama":"Mulla Y, Avellaneda Sarrió M, Roland A, et al. Weak catch bonds make strong networks. <i>Nature Materials</i>. 2022;21(9):1019-1023. doi:<a href=\"https://doi.org/10.1038/s41563-022-01288-0\">10.1038/s41563-022-01288-0</a>","chicago":"Mulla, Yuval, Mario Avellaneda Sarrió, Antoine Roland, Lucia Baldauf, Wonyeong Jung, Taeyoon Kim, Sander J. Tans, and Gijsje H. Koenderink. “Weak Catch Bonds Make Strong Networks.” <i>Nature Materials</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41563-022-01288-0\">https://doi.org/10.1038/s41563-022-01288-0</a>.","apa":"Mulla, Y., Avellaneda Sarrió, M., Roland, A., Baldauf, L., Jung, W., Kim, T., … Koenderink, G. H. (2022). Weak catch bonds make strong networks. <i>Nature Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41563-022-01288-0\">https://doi.org/10.1038/s41563-022-01288-0</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"09","external_id":{"pmid":["36008604"],"isi":["000844592000002"]},"page":"1019-1023","acknowledgement":"We thank M. van Hecke and C. Alkemade for critical reading of the manuscript. We thank P. R. ten Wolde, K. Storm, W. Ellenbroek, C. Broedersz, D. Brueckner and M. Berger for fruitful discussions. We thank W. Brieher and V. Tang from the University of Illinois for the kind gift of purified α-actinin-4 (WT and the K255E point mutant) and their plasmids; M. Kuit-Vinkenoog and J. den Haan for actin and further purification of α-actinin-4; A. Goutou and I. Isturiz-Petitjean for co-sedimentation measurements and V. Sunderlíková for the design, mutagenesis, cloning and purifying of the α-actinin-4 constructs used in the single-molecule experiments. We gratefully acknowledge financial support from the following sources: research program of the Netherlands Organization for Scientific Research (NWO) (S.J.T., A.R. and M.J.A.); ERC Starting Grant (335672-MINICELL) (G.H.K. and Y.M.). ‘BaSyC—Building a Synthetic Cell’ Gravitation grant (024.003.019) of the Netherlands Ministry of Education, Culture and Science (OCW) and the Netherlands Organisation for Scientific Research (G.H.K. and L.B.); and support from the National Institutes of Health (1R01GM126256) (T.K. and W.J.).","publication_identifier":{"issn":["1476-1122"],"eissn":["1476-4660"]},"isi":1,"status":"public","doi":"10.1038/s41563-022-01288-0","publication_status":"published","oa_version":"Preprint","type":"journal_article","author":[{"first_name":"Yuval","last_name":"Mulla","full_name":"Mulla, Yuval"},{"id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","orcid":"0000-0001-6406-524X","first_name":"Mario","full_name":"Avellaneda Sarrió, Mario","last_name":"Avellaneda Sarrió"},{"full_name":"Roland, Antoine","last_name":"Roland","first_name":"Antoine"},{"first_name":"Lucia","full_name":"Baldauf, Lucia","last_name":"Baldauf"},{"full_name":"Jung, Wonyeong","last_name":"Jung","first_name":"Wonyeong"},{"full_name":"Kim, Taeyoon","last_name":"Kim","first_name":"Taeyoon"},{"first_name":"Sander J.","last_name":"Tans","full_name":"Tans, Sander J."},{"first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H.","last_name":"Koenderink"}],"article_processing_charge":"No","date_updated":"2023-08-03T14:08:47Z","department":[{"_id":"MiSi"}]},{"article_processing_charge":"No","author":[{"last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","first_name":"Rishabh"},{"last_name":"Hease","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","first_name":"William J"},{"orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"last_name":"Arnold","full_name":"Arnold, Georg M","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876"},{"id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","orcid":"0000-0003-4345-4267","first_name":"Liu","last_name":"Qiu","full_name":"Qiu, Liu"},{"full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M"}],"department":[{"_id":"JoFi"}],"year":"2022","date_updated":"2024-10-09T21:03:27Z","date_published":"2022-05-01T00:00:00Z","status":"public","oa_version":"None","type":"conference","quality_controlled":"1","doi":"10.1364/CLEO_QELS.2022.FW4D.4","abstract":[{"text":"We present a quantum-enabled microwave-telecom interface with bidirectional conversion efficiencies up to 15% and added input noise quanta as low as 0.16. Moreover, we observe evidence for electro-optic laser cooling and vacuum amplification.","lang":"eng"}],"date_created":"2022-09-11T22:01:58Z","publication_status":"published","title":"Realizing a quantum-enabled interconnect between microwave and telecom light","conference":{"end_date":"2022-05-20","name":"CLEO: QELS Fundamental Science","start_date":"2022-05-15","location":"San Jose, CA, United States"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"isbn":["9781557528209"]},"publication":"Conference on Lasers and Electro-Optics","language":[{"iso":"eng"}],"article_number":"FW4D.4","citation":{"mla":"Sahu, Rishabh, et al. “Realizing a Quantum-Enabled Interconnect between Microwave and Telecom Light.” <i>Conference on Lasers and Electro-Optics</i>, FW4D.4, Optica Publishing Group, 2022, doi:<a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">10.1364/CLEO_QELS.2022.FW4D.4</a>.","ista":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Realizing a quantum-enabled interconnect between microwave and telecom light. Conference on Lasers and Electro-Optics. CLEO: QELS Fundamental Science, FW4D.4.","short":"R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2022.","ieee":"R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Realizing a quantum-enabled interconnect between microwave and telecom light,” in <i>Conference on Lasers and Electro-Optics</i>, San Jose, CA, United States, 2022.","ama":"Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Realizing a quantum-enabled interconnect between microwave and telecom light. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2022. doi:<a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">10.1364/CLEO_QELS.2022.FW4D.4</a>","chicago":"Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Realizing a Quantum-Enabled Interconnect between Microwave and Telecom Light.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2022. <a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4</a>.","apa":"Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., &#38; Fink, J. M. (2022). Realizing a quantum-enabled interconnect between microwave and telecom light. In <i>Conference on Lasers and Electro-Optics</i>. San Jose, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4\">https://doi.org/10.1364/CLEO_QELS.2022.FW4D.4</a>"},"day":"01","publisher":"Optica Publishing Group","corr_author":"1","scopus_import":"1","_id":"12088"},{"volume":250,"ec_funded":1,"title":"Algorithms and hardness results for computing cores of Markov chains","publication":"42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science","ddc":["000"],"_id":"12102","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"14","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)"},"oa":1,"date_published":"2022-12-14T00:00:00Z","year":"2022","abstract":[{"lang":"eng","text":"Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset."}],"date_created":"2023-01-01T23:00:50Z","intvolume":"       250","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","conference":{"end_date":"2022-12-20","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2022-12-18","location":"Madras, India"},"file":[{"content_type":"application/pdf","creator":"dernst","date_created":"2023-01-20T10:39:44Z","access_level":"open_access","success":1,"file_id":"12324","file_size":872534,"checksum":"6660c802489013f034c9e8bd57f4d46e","relation":"main_file","file_name":"2022_LIPICs_Ahmadi.pdf","date_updated":"2023-01-20T10:39:44Z"}],"acknowledgement":"The research was partially supported by the Hong Kong Research Grants Council ECS\r\nProject No. 26208122, ERC CoG 863818 (FoRM-SMArt), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385, HKUST– Kaisa Joint Research Institute Project Grant HKJRI3A-055 and HKUST Startup Grant R9272. Ali Ahmadi and Roodabeh Safavi were interns at HKUST.","publication_identifier":{"isbn":["9783959772617"],"issn":["1868-8969"]},"citation":{"short":"A. Ahmadi, K. Chatterjee, A.K. Goharshady, T. Meggendorfer, R. Safavi Hemami, D. Zikelic, in:, 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.","ieee":"A. Ahmadi, K. Chatterjee, A. K. Goharshady, T. Meggendorfer, R. Safavi Hemami, and D. Zikelic, “Algorithms and hardness results for computing cores of Markov chains,” in <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Madras, India, 2022, vol. 250.","ista":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. 2022. Algorithms and hardness results for computing cores of Markov chains. 42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science. FSTTCS: Foundations of Software Technology and Theoretical Computer Science vol. 250, 29.","mla":"Ahmadi, Ali, et al. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, vol. 250, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>.","ama":"Ahmadi A, Chatterjee K, Goharshady AK, Meggendorfer T, Safavi Hemami R, Zikelic D. Algorithms and hardness results for computing cores of Markov chains. In: <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>. Vol 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">10.4230/LIPIcs.FSTTCS.2022.29</a>","apa":"Ahmadi, A., Chatterjee, K., Goharshady, A. K., Meggendorfer, T., Safavi Hemami, R., &#38; Zikelic, D. (2022). Algorithms and hardness results for computing cores of Markov chains. In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i> (Vol. 250). Madras, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>","chicago":"Ahmadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Tobias Meggendorfer, Roodabeh Safavi Hemami, and Dorde Zikelic. “Algorithms and Hardness Results for Computing Cores of Markov Chains.” In <i>42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science</i>, Vol. 250. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29\">https://doi.org/10.4230/LIPIcs.FSTTCS.2022.29</a>."},"article_number":"29","has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2023-01-20T10:39:44Z","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"author":[{"last_name":"Ahmadi","full_name":"Ahmadi, Ali","first_name":"Ali"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"},{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165"},{"first_name":"Roodabeh","id":"72ed2640-8972-11ed-ae7b-f9c81ec75154","last_name":"Safavi Hemami","full_name":"Safavi Hemami, Roodabeh"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde"}],"article_processing_charge":"No","date_updated":"2025-07-10T11:50:23Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"status":"public","publication_status":"published","doi":"10.4230/LIPIcs.FSTTCS.2022.29","type":"conference","oa_version":"Published Version"},{"article_processing_charge":"No","author":[{"first_name":"Rémy","last_name":"Roca","full_name":"Roca, Rémy"},{"last_name":"De Meyer","full_name":"De Meyer, Victorien","first_name":"Victorien"},{"last_name":"Muller","full_name":"Muller, Caroline J","first_name":"Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"date_updated":"2023-08-03T14:10:27Z","department":[{"_id":"CaMu"}],"isi":1,"status":"public","doi":"10.1029/2022GL100624","publication_status":"published","oa_version":"Published Version","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","external_id":{"isi":["000924587900001"]},"acknowledgement":"We thank S. Cloché for her support with the handling of these various data sets. This study benefited from the IPSL mesocenter ESPRI facility which is supported by CNRS, UPMC, Labex L-IPSL, CNES and Ecole Polytechnique. We thank Rômulo A. Jucá Oliveira and Thomas\r\nFiolleau for helpful discussions on satellite data and precipitation. The authors acknowledge the CNES and CNRS support under the Megha-Tropiques program. C.M. gratefully acknowledges\r\nfunding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Project CLUSTER, Grant agreement 805041). We further\r\nthank the reviewers for their insightful comments that improved the paper.","file":[{"content_type":"application/pdf","creator":"dernst","success":1,"access_level":"open_access","date_created":"2023-01-20T10:52:31Z","file_id":"12326","file_size":875379,"relation":"main_file","checksum":"2c6325cea8938adeea7e3a6f5c2ab64e","date_updated":"2023-01-20T10:52:31Z","file_name":"2022_GeophysicalResearchLetters_Roca.pdf"}],"publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"has_accepted_license":"1","article_number":"e2022GL100624","citation":{"ieee":"R. Roca, V. De Meyer, and C. J. Muller, “Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans,” <i>Geophysical Research Letters</i>, vol. 49, no. 24. Wiley, 2022.","ista":"Roca R, De Meyer V, Muller CJ. 2022. Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. Geophysical Research Letters. 49(24), e2022GL100624.","short":"R. Roca, V. De Meyer, C.J. Muller, Geophysical Research Letters 49 (2022).","mla":"Roca, Rémy, et al. “Precipitating Fraction, Not Intensity, Explains Extreme Coarse-Grained Precipitation Clausius-Clapeyron Scaling with Sea Surface Temperature over Tropical Oceans.” <i>Geophysical Research Letters</i>, vol. 49, no. 24, e2022GL100624, Wiley, 2022, doi:<a href=\"https://doi.org/10.1029/2022GL100624\">10.1029/2022GL100624</a>.","ama":"Roca R, De Meyer V, Muller CJ. Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. <i>Geophysical Research Letters</i>. 2022;49(24). doi:<a href=\"https://doi.org/10.1029/2022GL100624\">10.1029/2022GL100624</a>","apa":"Roca, R., De Meyer, V., &#38; Muller, C. J. (2022). Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans. <i>Geophysical Research Letters</i>. Wiley. <a href=\"https://doi.org/10.1029/2022GL100624\">https://doi.org/10.1029/2022GL100624</a>","chicago":"Roca, Rémy, Victorien De Meyer, and Caroline J Muller. “Precipitating Fraction, Not Intensity, Explains Extreme Coarse-Grained Precipitation Clausius-Clapeyron Scaling with Sea Surface Temperature over Tropical Oceans.” <i>Geophysical Research Letters</i>. Wiley, 2022. <a href=\"https://doi.org/10.1029/2022GL100624\">https://doi.org/10.1029/2022GL100624</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2023-01-20T10:52:31Z","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"date_published":"2022-12-28T00:00:00Z","issue":"24","year":"2022","intvolume":"        49","abstract":[{"lang":"eng","text":"The sensitivity of coarse-grained daily extreme precipitation to sea surface temperature is analyzed using satellite precipitation estimates over the 300–302.5 K range. A theoretical scaling is proposed, linking changes in coarse-grained precipitation to changes in fine-scale hourly precipitation area fraction and changes in conditional fine-scale precipitation rates. The analysis reveals that the extreme coarse-grained precipitation scaling with temperature (∼7%/K) is dominated by the fine-scale precipitating fraction scaling (∼6.5%/K) when using a 3 mm/h fine-scale threshold to delineate the precipitating fraction. These results are shown to be robust to the selection of the precipitation product and to the percentile used to characterize the extreme. This new coarse-grained scaling is further related to the well-known scaling for fine-scale precipitation extremes, and suggests a compensation between thermodynamic and dynamic contributions or that both contributions are small with respect to that of fractional coverage. These results suggest that processes responsible for the changes in fractional coverage are to be accounted for to assess the sensitivity of coarse-grained extreme daily precipitation to surface temperature."}],"date_created":"2023-01-08T23:00:53Z","quality_controlled":"1","volume":49,"article_type":"letter_note","title":"Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans","publication":"Geophysical Research Letters","ddc":["550"],"_id":"12107","day":"28","publisher":"Wiley"},{"oa":1,"date_published":"2022-12-23T00:00:00Z","year":"2022","issue":"26","date_created":"2023-01-08T23:00:53Z","abstract":[{"lang":"eng","text":"The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation."}],"intvolume":"       129","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"quality_controlled":"1","volume":129,"ec_funded":1,"article_type":"original","title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","publication":"Physical Review Letters","pmid":1,"_id":"12108","publisher":"American Physical Society","day":"23","author":[{"last_name":"Meadowcroft","full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie"},{"first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","full_name":"Palaia, Ivan"},{"full_name":"Pfitzner, Anna Katharina","last_name":"Pfitzner","first_name":"Anna Katharina"},{"first_name":"Aurélien","last_name":"Roux","full_name":"Roux, Aurélien"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}],"article_processing_charge":"No","date_updated":"2025-04-14T07:54:53Z","department":[{"_id":"AnSa"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1103/PhysRevLett.129.268101","type":"journal_article","oa_version":"Preprint","month":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank T. C. T. Michaels and J. Palacci for useful discussions. We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge funding by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P., and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). ","external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"citation":{"mla":"Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>, vol. 129, no. 26, 268101, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>.","ista":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. 129(26), 268101.","ieee":"B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić, “Mechanochemical rules for shape-shifting filaments that remodel membranes,” <i>Physical Review Letters</i>, vol. 129, no. 26. American Physical Society, 2022.","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","chicago":"Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>.","apa":"Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., &#38; Šarić, A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>","ama":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. 2022;129(26). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>"},"article_number":"268101","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","file":[{"content_type":"application/pdf","creator":"dernst","file_id":"12327","date_created":"2023-01-20T11:58:59Z","access_level":"open_access","success":1,"checksum":"5150287295e0ce4f12462c990744d65d","relation":"main_file","file_size":5436804,"file_name":"2022_JourMathPhysics_Henheik.pdf","date_updated":"2023-01-20T11:58:59Z"}],"acknowledgement":"J.H. gratefully acknowledges the partial financial support by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331.\r\n","external_id":{"isi":["000900748900002"]},"publication_identifier":{"issn":["0022-2488"]},"citation":{"mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12, 122302, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>.","ista":"Henheik SJ, Tumulka R. 2022. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. Journal of Mathematical Physics. 63(12), 122302.","short":"S.J. Henheik, R. Tumulka, Journal of Mathematical Physics 63 (2022).","ieee":"S. J. Henheik and R. Tumulka, “Interior-boundary conditions for the Dirac equation at point sources in three dimensions,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 12. AIP Publishing, 2022.","chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Interior-Boundary Conditions for the Dirac Equation at Point Sources in Three Dimensions.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>.","apa":"Henheik, S. J., &#38; Tumulka, R. (2022). Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0104675\">https://doi.org/10.1063/5.0104675</a>","ama":"Henheik SJ, Tumulka R. Interior-boundary conditions for the Dirac equation at point sources in three dimensions. <i>Journal of Mathematical Physics</i>. 2022;63(12). doi:<a href=\"https://doi.org/10.1063/5.0104675\">10.1063/5.0104675</a>"},"article_number":"122302","has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2023-01-20T11:58:59Z","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331"}],"author":[{"orcid":"0000-0003-1106-327X","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","last_name":"Henheik","full_name":"Henheik, Sven Joscha"},{"full_name":"Tumulka, Roderich","last_name":"Tumulka","first_name":"Roderich"}],"article_processing_charge":"No","date_updated":"2025-04-14T07:57:18Z","department":[{"_id":"LaEr"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1063/5.0104675","type":"journal_article","oa_version":"Published Version","volume":63,"ec_funded":1,"title":"Interior-boundary conditions for the Dirac equation at point sources in three dimensions","article_type":"original","publication":"Journal of Mathematical Physics","ddc":["510"],"_id":"12110","publisher":"AIP Publishing","day":"01","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)"},"oa":1,"date_published":"2022-12-01T00:00:00Z","year":"2022","issue":"12","date_created":"2023-01-08T23:00:53Z","intvolume":"        63","abstract":[{"lang":"eng","text":"A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, i.e., for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has successfully been done already in one space dimension, and more generally for codimension-1 boundaries, the situation of point sources in three dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3D, which also correspond to a boundary condition. Indeed, we confirm this expectation here by proving that there is no self-adjoint operator on a (truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with an IBC (on the boundary consisting of configurations with a particle at the origin) that are away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential."}],"quality_controlled":"1"}]