[{"external_id":{"pmid":["25675085"]},"author":[{"full_name":"Li, Haixing","last_name":"Li","first_name":"Haixing"},{"full_name":"Su, Timothy A.","first_name":"Timothy A.","last_name":"Su"},{"last_name":"Zhang","first_name":"Vivian","full_name":"Zhang, Vivian"},{"last_name":"Steigerwald","first_name":"Michael L.","full_name":"Steigerwald, Michael L."},{"full_name":"Nuckolls, Colin","first_name":"Colin","last_name":"Nuckolls"},{"first_name":"Latha","last_name":"Venkataraman","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf"}],"abstract":[{"text":"Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S–Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor–acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level.","lang":"eng"}],"extern":"1","_id":"17973","oa_version":"None","page":"5028-5033","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","volume":137,"publication_status":"published","date_updated":"2024-12-18T12:10:06Z","publication":"Journal of the American Chemical Society","quality_controlled":"1","article_processing_charge":"No","publisher":"American Chemical Society","language":[{"iso":"eng"}],"pmid":1,"month":"02","intvolume":"       137","citation":{"short":"H. Li, T.A. Su, V. Zhang, M.L. Steigerwald, C. Nuckolls, L. Venkataraman, Journal of the American Chemical Society 137 (2015) 5028–5033.","ista":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. 2015. Electric field breakdown in single molecule junctions. Journal of the American Chemical Society. 137(15), 5028–5033.","apa":"Li, H., Su, T. A., Zhang, V., Steigerwald, M. L., Nuckolls, C., &#38; Venkataraman, L. (2015). Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>","mla":"Li, Haixing, et al. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15, American Chemical Society, 2015, pp. 5028–33, doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>.","ieee":"H. Li, T. A. Su, V. Zhang, M. L. Steigerwald, C. Nuckolls, and L. Venkataraman, “Electric field breakdown in single molecule junctions,” <i>Journal of the American Chemical Society</i>, vol. 137, no. 15. American Chemical Society, pp. 5028–5033, 2015.","chicago":"Li, Haixing, Timothy A. Su, Vivian Zhang, Michael L. Steigerwald, Colin Nuckolls, and Latha Venkataraman. “Electric Field Breakdown in Single Molecule Junctions.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/ja512523r\">https://doi.org/10.1021/ja512523r</a>.","ama":"Li H, Su TA, Zhang V, Steigerwald ML, Nuckolls C, Venkataraman L. Electric field breakdown in single molecule junctions. <i>Journal of the American Chemical Society</i>. 2015;137(15):5028-5033. doi:<a href=\"https://doi.org/10.1021/ja512523r\">10.1021/ja512523r</a>"},"date_published":"2015-02-12T00:00:00Z","status":"public","doi":"10.1021/ja512523r","date_created":"2024-09-09T10:04:02Z","day":"12","type":"journal_article","issue":"15","title":"Electric field breakdown in single molecule junctions","OA_type":"closed access","scopus_import":"1","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]}},{"scopus_import":"1","publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"issue":"4","title":"Molecular wires","OA_type":"closed access","day":"30","type":"journal_article","status":"public","date_created":"2024-09-09T10:53:55Z","doi":"10.1039/c5cs90010g","citation":{"short":"D.M. Guldi, H. Nishihara, L. Venkataraman, Chemical Society Reviews 44 (2015) 842–844.","apa":"Guldi, D. M., Nishihara, H., &#38; Venkataraman, L. (2015). Molecular wires. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>","ista":"Guldi DM, Nishihara H, Venkataraman L. 2015. Molecular wires. Chemical Society Reviews. 44(4), 842–844.","mla":"Guldi, Dirk M., et al. “Molecular Wires.” <i>Chemical Society Reviews</i>, vol. 44, no. 4, Royal Society of Chemistry, 2015, pp. 842–44, doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>.","ama":"Guldi DM, Nishihara H, Venkataraman L. Molecular wires. <i>Chemical Society Reviews</i>. 2015;44(4):842-844. doi:<a href=\"https://doi.org/10.1039/c5cs90010g\">10.1039/c5cs90010g</a>","ieee":"D. M. Guldi, H. Nishihara, and L. Venkataraman, “Molecular wires,” <i>Chemical Society Reviews</i>, vol. 44, no. 4. Royal Society of Chemistry, pp. 842–844, 2015.","chicago":"Guldi, Dirk M., Hiroshi Nishihara, and Latha Venkataraman. “Molecular Wires.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2015. <a href=\"https://doi.org/10.1039/c5cs90010g\">https://doi.org/10.1039/c5cs90010g</a>."},"date_published":"2015-01-30T00:00:00Z","intvolume":"        44","publisher":"Royal Society of Chemistry","language":[{"iso":"eng"}],"month":"01","pmid":1,"publication":"Chemical Society Reviews","quality_controlled":"1","article_processing_charge":"No","date_updated":"2025-01-02T13:26:36Z","year":"2015","volume":44,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"842-844","article_type":"letter_note","_id":"17974","oa_version":"None","external_id":{"pmid":["25636152"]},"author":[{"first_name":"Dirk M.","last_name":"Guldi","full_name":"Guldi, Dirk M."},{"full_name":"Nishihara, Hiroshi","last_name":"Nishihara","first_name":"Hiroshi"},{"id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha","last_name":"Venkataraman","first_name":"Latha"}],"abstract":[{"text":"Guest editors Dirk M. Guldi, Hiroshi Nishihara and Latha Venkataraman introduce the Molecular Wires issue of \"Chemical Society Reviews\".","lang":"eng"}],"extern":"1"},{"article_type":"original","page":"215-220","_id":"17975","oa_version":"None","external_id":{"pmid":["25698330"]},"author":[{"first_name":"Timothy A.","last_name":"Su","full_name":"Su, Timothy A."},{"last_name":"Li","first_name":"Haixing","full_name":"Li, Haixing"},{"first_name":"Michael L.","last_name":"Steigerwald","full_name":"Steigerwald, Michael L."},{"last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha","orcid":"0000-0002-6957-6089"},{"last_name":"Nuckolls","first_name":"Colin","full_name":"Nuckolls, Colin"}],"extern":"1","abstract":[{"text":"A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur–methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.","lang":"eng"}],"date_updated":"2025-01-02T13:28:51Z","volume":7,"year":"2015","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T.A. Su, H. Li, M.L. Steigerwald, L. Venkataraman, C. Nuckolls, Nature Chemistry 7 (2015) 215–220.","ista":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. 2015. Stereoelectronic switching in single-molecule junctions. Nature Chemistry. 7(3), 215–220.","apa":"Su, T. A., Li, H., Steigerwald, M. L., Venkataraman, L., &#38; Nuckolls, C. (2015). Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>","mla":"Su, Timothy A., et al. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 215–20, doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>.","ama":"Su TA, Li H, Steigerwald ML, Venkataraman L, Nuckolls C. Stereoelectronic switching in single-molecule junctions. <i>Nature Chemistry</i>. 2015;7(3):215-220. doi:<a href=\"https://doi.org/10.1038/nchem.2180\">10.1038/nchem.2180</a>","ieee":"T. A. Su, H. Li, M. L. Steigerwald, L. Venkataraman, and C. Nuckolls, “Stereoelectronic switching in single-molecule junctions,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 215–220, 2015.","chicago":"Su, Timothy A., Haixing Li, Michael L. Steigerwald, Latha Venkataraman, and Colin Nuckolls. “Stereoelectronic Switching in Single-Molecule Junctions.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2180\">https://doi.org/10.1038/nchem.2180</a>."},"date_published":"2015-02-16T00:00:00Z","intvolume":"         7","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"02","pmid":1,"publication":"Nature Chemistry","quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"title":"Stereoelectronic switching in single-molecule junctions","issue":"3","OA_type":"closed access","type":"journal_article","day":"16","status":"public","doi":"10.1038/nchem.2180","date_created":"2024-09-09T10:54:59Z"},{"date_updated":"2025-01-02T13:35:46Z","year":"2015","volume":7,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"209-214","article_type":"original","_id":"17976","oa_version":"None","external_id":{"pmid":["25698329"]},"author":[{"last_name":"Dell","first_name":"Emma J.","full_name":"Dell, Emma J."},{"full_name":"Capozzi, Brian","first_name":"Brian","last_name":"Capozzi"},{"first_name":"Jianlong","last_name":"Xia","full_name":"Xia, Jianlong"},{"last_name":"Venkataraman","first_name":"Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089","full_name":"Venkataraman, Latha"},{"first_name":"Luis M.","last_name":"Campos","full_name":"Campos, Luis M."}],"extern":"1","abstract":[{"lang":"eng","text":"To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials."}],"publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"scopus_import":"1","issue":"3","title":"Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes","OA_type":"closed access","day":"02","type":"journal_article","status":"public","date_created":"2024-09-09T10:55:42Z","doi":"10.1038/nchem.2160","citation":{"ista":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. 2015. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. Nature Chemistry. 7(3), 209–214.","apa":"Dell, E. J., Capozzi, B., Xia, J., Venkataraman, L., &#38; Campos, L. M. (2015). Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>","short":"E.J. Dell, B. Capozzi, J. Xia, L. Venkataraman, L.M. Campos, Nature Chemistry 7 (2015) 209–214.","ama":"Dell EJ, Capozzi B, Xia J, Venkataraman L, Campos LM. Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes. <i>Nature Chemistry</i>. 2015;7(3):209-214. doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>","chicago":"Dell, Emma J., Brian Capozzi, Jianlong Xia, Latha Venkataraman, and Luis M. Campos. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nchem.2160\">https://doi.org/10.1038/nchem.2160</a>.","ieee":"E. J. Dell, B. Capozzi, J. Xia, L. Venkataraman, and L. M. Campos, “Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes,” <i>Nature Chemistry</i>, vol. 7, no. 3. Springer Nature, pp. 209–214, 2015.","mla":"Dell, Emma J., et al. “Molecular Length Dictates the Nature of Charge Carriers in Single-Molecule Junctions of Oxidized Oligothiophenes.” <i>Nature Chemistry</i>, vol. 7, no. 3, Springer Nature, 2015, pp. 209–14, doi:<a href=\"https://doi.org/10.1038/nchem.2160\">10.1038/nchem.2160</a>."},"date_published":"2015-02-02T00:00:00Z","intvolume":"         7","publisher":"Springer Nature","language":[{"iso":"eng"}],"pmid":1,"month":"02","publication":"Nature Chemistry","quality_controlled":"1","article_processing_charge":"No"},{"conference":{"location":"Portland, OR, United States","start_date":"2015-06-14","end_date":"2015-06-17","name":"STOC: Symposium on the Theory of Computing"},"citation":{"apa":"Alwen, J. F., &#38; Serbinenko, V. (2015). High parallel complexity graphs and memory-hard functions. In <i>Proceedings of the 47th annual ACM symposium on Theory of computing</i> (pp. 595–603). Portland, OR, United States: ACM. <a href=\"https://doi.org/10.1145/2746539.2746622\">https://doi.org/10.1145/2746539.2746622</a>","ista":"Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard functions. Proceedings of the 47th annual ACM symposium on Theory of computing. STOC: Symposium on the Theory of Computing, 595–603.","short":"J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603.","ieee":"J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard functions,” in <i>Proceedings of the 47th annual ACM symposium on Theory of computing</i>, Portland, OR, United States, 2015, pp. 595–603.","chicago":"Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” In <i>Proceedings of the 47th Annual ACM Symposium on Theory of Computing</i>, 595–603. ACM, 2015. <a href=\"https://doi.org/10.1145/2746539.2746622\">https://doi.org/10.1145/2746539.2746622</a>.","ama":"Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions. In: <i>Proceedings of the 47th Annual ACM Symposium on Theory of Computing</i>. ACM; 2015:595-603. doi:<a href=\"https://doi.org/10.1145/2746539.2746622\">10.1145/2746539.2746622</a>","mla":"Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” <i>Proceedings of the 47th Annual ACM Symposium on Theory of Computing</i>, ACM, 2015, pp. 595–603, doi:<a href=\"https://doi.org/10.1145/2746539.2746622\">10.1145/2746539.2746622</a>."},"date_published":"2015-06-01T00:00:00Z","publication":"Proceedings of the 47th annual ACM symposium on Theory of computing","quality_controlled":"1","article_processing_charge":"No","publisher":"ACM","language":[{"iso":"eng"}],"month":"06","title":"High parallel complexity graphs and memory-hard functions","scopus_import":"1","publist_id":"5498","corr_author":"1","status":"public","das_tickbox":"1","date_created":"2018-12-11T11:53:16Z","main_file_link":[{"url":"http://eprint.iacr.org/2014/238","open_access":"1"}],"doi":"10.1145/2746539.2746622","type":"conference","day":"01","project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"_id":"1652","ec_funded":1,"oa_version":"Submitted Version","page":"595 - 603","oa":1,"external_id":{"isi":["000485296600063"],"cryptoeprintid":["2014/238"]},"author":[{"last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"full_name":"Serbinenko, Vladimir","first_name":"Vladimir","last_name":"Serbinenko"}],"abstract":[{"lang":"eng","text":"We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp."}],"department":[{"_id":"KrPi"}],"date_updated":"2026-06-22T14:08:55Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","cryptoeprintid":1,"publication_status":"published"},{"citation":{"mla":"Demay, Grégory, et al. <i>Query-Complexity Amplification for Random Oracles</i>. Vol. 9063, Springer, 2015, pp. 159–80, doi:<a href=\"https://doi.org/10.1007/978-3-319-17470-9_10\">10.1007/978-3-319-17470-9_10</a>.","chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity Amplification for Random Oracles,” 9063:159–80. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-17470-9_10\">https://doi.org/10.1007/978-3-319-17470-9_10</a>.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification for random oracles,” presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for random oracles. In: Vol 9063. Springer; 2015:159-180. doi:<a href=\"https://doi.org/10.1007/978-3-319-17470-9_10\">10.1007/978-3-319-17470-9_10</a>","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification for random oracles. ICITS: International Conference on Information Theoretic Security, LNCS, vol. 9063, 159–180.","apa":"Demay, G., Gazi, P., Maurer, U., &#38; Tackmann, B. (2015). Query-complexity amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-17470-9_10\">https://doi.org/10.1007/978-3-319-17470-9_10</a>"},"date_published":"2015-01-01T00:00:00Z","conference":{"name":"ICITS: International Conference on Information Theoretic Security","end_date":"2015-05-05","location":"Lugano, Switzerland","start_date":"2015-05-02"},"intvolume":"      9063","month":"01","publisher":"Springer","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publist_id":"5507","scopus_import":"1","title":"Query-complexity amplification for random oracles","day":"01","type":"conference","main_file_link":[{"url":"http://eprint.iacr.org/2015/315","open_access":"1"}],"doi":"10.1007/978-3-319-17470-9_10","date_created":"2018-12-11T11:53:13Z","status":"public","das_tickbox":"1","oa":1,"page":"159 - 180","oa_version":"Submitted Version","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"1644","ec_funded":1,"department":[{"_id":"KrPi"}],"abstract":[{"text":"Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r &lt; R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c.","lang":"eng"}],"external_id":{"isi":["000362493000011"],"cryptoeprintid":["2015/315"]},"author":[{"last_name":"Demay","first_name":"Grégory","full_name":"Demay, Grégory"},{"first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maurer","first_name":"Ueli","full_name":"Maurer, Ueli"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"alternative_title":["LNCS"],"date_updated":"2026-06-22T14:08:28Z","publication_status":"published","year":"2015","volume":9063,"cryptoeprintid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1},{"corr_author":"1","scopus_import":"1","publist_id":"5481","title":"Relaxing full-codebook security: A refined analysis of key-length extension schemes","day":"12","type":"conference","main_file_link":[{"url":"http://eprint.iacr.org/2015/397","open_access":"1"}],"doi":"10.1007/978-3-662-48116-5_16","date_created":"2018-12-11T11:53:22Z","das_tickbox":"1","status":"public","date_published":"2015-08-12T00:00:00Z","citation":{"mla":"Gazi, Peter, et al. <i>Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes</i>. Vol. 9054, Springer, 2015, pp. 319–41, doi:<a href=\"https://doi.org/10.1007/978-3-662-48116-5_16\">10.1007/978-3-662-48116-5_16</a>.","chicago":"Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-662-48116-5_16\">https://doi.org/10.1007/978-3-662-48116-5_16</a>.","ieee":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook security: A refined analysis of key-length extension schemes,” vol. 9054. Springer, pp. 319–341, 2015.","ama":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 2015;9054:319-341. doi:<a href=\"https://doi.org/10.1007/978-3-662-48116-5_16\">10.1007/978-3-662-48116-5_16</a>","short":"P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341.","apa":"Gazi, P., Lee, J., Seurin, Y., Steinberger, J., &#38; Tessaro, S. (2015). Relaxing full-codebook security: A refined analysis of key-length extension schemes. Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. <a href=\"https://doi.org/10.1007/978-3-662-48116-5_16\">https://doi.org/10.1007/978-3-662-48116-5_16</a>","ista":"Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 9054, 319–341."},"conference":{"start_date":"2015-03-08","location":"Istanbul, Turkey","name":"FSE: Fast Software Encryption","end_date":"2015-03-11"},"intvolume":"      9054","month":"08","language":[{"iso":"eng"}],"publisher":"Springer","article_processing_charge":"No","quality_controlled":"1","alternative_title":["LNCS"],"series_title":"Lecture Notes in Computer Science","date_updated":"2026-06-22T14:09:37Z","publication_status":"published","cryptoeprintid":1,"volume":9054,"year":"2015","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"page":"319 - 341","oa_version":"Submitted Version","_id":"1668","project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"ec_funded":1,"department":[{"_id":"KrPi"}],"abstract":[{"text":"We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.\r\nMore concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži and Tessaro’s two-call ","lang":"eng"}],"author":[{"last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"last_name":"Lee","first_name":"Jooyoung","full_name":"Lee, Jooyoung"},{"last_name":"Seurin","first_name":"Yannick","full_name":"Seurin, Yannick"},{"full_name":"Steinberger, John","first_name":"John","last_name":"Steinberger"},{"full_name":"Tessaro, Stefano","first_name":"Stefano","last_name":"Tessaro"}],"external_id":{"isi":["000363765800016"],"cryptoeprintid":["2015/397"]}},{"date_updated":"2026-06-22T22:30:18Z","file_date_updated":"2020-07-14T12:45:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"related_material":{"record":[{"id":"9711","status":"public","relation":"research_data"},{"id":"9765","relation":"research_data","status":"public"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"file":[{"creator":"system","checksum":"0e82e3279f50b15c6c170c042627802b","date_created":"2018-12-12T10:09:00Z","access_level":"open_access","file_size":1387760,"date_updated":"2020-07-14T12:45:07Z","relation":"main_file","file_id":"4723","content_type":"application/pdf","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf"}],"pubrep_id":"468","publication_status":"published","volume":13,"year":"2015","oa_version":"Published Version","_id":"1619","project":[{"name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"},{"name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","call_identifier":"FP7","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa":1,"abstract":[{"lang":"eng","text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution."}],"external_id":{"isi":["000365898900011"]},"author":[{"first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marta","last_name":"Dravecka","orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Batur, Tugce","first_name":"Tugce","last_name":"Batur"},{"full_name":"Guvenek, Aysegul","last_name":"Guvenek","first_name":"Aysegul"},{"first_name":"Dilay","last_name":"Ayhan","full_name":"Ayhan, Dilay"},{"full_name":"Toprak, Erdal","first_name":"Erdal","last_name":"Toprak"},{"last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"}],"department":[{"_id":"ToBo"}],"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","issue":"11","publist_id":"5547","scopus_import":"1","corr_author":"1","ddc":["570"],"date_created":"2018-12-11T11:53:04Z","doi":"10.1371/journal.pbio.1002299","status":"public","has_accepted_license":"1","type":"journal_article","day":"18","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e1002299","intvolume":"        13","citation":{"apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., &#38; Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>.","ieee":"G. Chevereau <i>et al.</i>, “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” <i>PLoS Biology</i>, vol. 13, no. 11. Public Library of Science, 2015.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. 2015;13(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>."},"date_published":"2015-11-18T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","publication":"PLoS Biology","month":"11","license":"https://creativecommons.org/licenses/by/4.0/","publisher":"Public Library of Science","language":[{"iso":"eng"}]},{"citation":{"short":"V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.","apa":"Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu242\">https://doi.org/10.1093/molbev/msu242</a>","ista":"Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025.","mla":"Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:<a href=\"https://doi.org/10.1093/molbev/msu242\">10.1093/molbev/msu242</a>.","ieee":"V. Seplyarskiy <i>et al.</i>, “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.","chicago":"Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/msu242\">https://doi.org/10.1093/molbev/msu242</a>.","ama":"Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. <i>Molecular Biology and Evolution</i>. 2014;31(11):3016-3025. doi:<a href=\"https://doi.org/10.1093/molbev/msu242\">10.1093/molbev/msu242</a>"},"date_published":"2014-11-01T00:00:00Z","page":"3016 - 3025","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"845","intvolume":"        31","month":"11","publisher":"Oxford University Press","quality_controlled":0,"extern":1,"abstract":[{"text":"Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.","lang":"eng"}],"publication":"Molecular Biology and Evolution","author":[{"full_name":"Seplyarskiy, Vladimir B","last_name":"Seplyarskiy","first_name":"Vladimir"},{"first_name":"Maria","last_name":"Logacheva","full_name":"Logacheva, Maria D"},{"full_name":"Penin, Aleksey A","last_name":"Penin","first_name":"Aleksey"},{"last_name":"Baranová","first_name":"Maria","full_name":"Baranová, Maria A"},{"last_name":"Leushkin","first_name":"Evgeny","full_name":"Leushkin, Evgeny V"},{"first_name":"Natalia","last_name":"Demidenko","full_name":"Demidenko, Natalia V"},{"full_name":"Klepikova, Anna V","first_name":"Anna","last_name":"Klepikova"},{"first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"},{"full_name":"James, Timothy Y","last_name":"James","first_name":"Timothy"}],"publist_id":"6801","issue":"11","title":"Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity","date_updated":"2021-01-12T08:19:21Z","publication_status":"published","day":"01","type":"journal_article","acknowledgement":"The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan.","year":"2014","volume":31,"doi":"10.1093/molbev/msu242","date_created":"2018-12-11T11:48:48Z","status":"public"},{"doi":"10.1021/ja5105987","date_created":"2020-09-18T10:07:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","day":"27","publication_status":"published","volume":136,"year":"2014","title":"Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan","issue":"51","date_updated":"2021-01-12T08:19:24Z","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis."}],"extern":"1","quality_controlled":"1","author":[{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Triboulet","first_name":"Sébastien","full_name":"Triboulet, Sébastien"},{"last_name":"Laguri","first_name":"Cédric","full_name":"Laguri, Cédric"},{"full_name":"Bougault, Catherine M.","last_name":"Bougault","first_name":"Catherine M."},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"first_name":"Morgane","last_name":"Callon","full_name":"Callon, Morgane"},{"last_name":"Arthur","first_name":"Michel","full_name":"Arthur, Michel"},{"full_name":"Simorre, Jean-Pierre","last_name":"Simorre","first_name":"Jean-Pierre"}],"publication":"Journal of the American Chemical Society","month":"11","language":[{"iso":"eng"}],"publisher":"American Chemical Society","oa_version":"None","_id":"8458","intvolume":"       136","date_published":"2014-11-27T00:00:00Z","citation":{"short":"P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon, M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014) 17852–17860.","ista":"Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M, Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. Journal of the American Chemical Society. 136(51), 17852–17860.","apa":"Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon, M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>","mla":"Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60, doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>.","ama":"Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan. <i>Journal of the American Chemical Society</i>. 2014;136(51):17852-17860. doi:<a href=\"https://doi.org/10.1021/ja5105987\">10.1021/ja5105987</a>","chicago":"Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault, Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial Peptidoglycan.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja5105987\">https://doi.org/10.1021/ja5105987</a>.","ieee":"P. Schanda <i>et al.</i>, “Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 51. American Chemical Society, pp. 17852–17860, 2014."},"article_type":"original","page":"17852-17860"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"url":"https://doi.org/10.1093/bioinformatics/btz397","relation":"erratum"}]},"publication_status":"published","year":"2014","volume":30,"keyword":["Statistics and Probability","Computational Theory and Mathematics","Biochemistry","Molecular Biology","Computational Mathematics","Computer Science Applications"],"date_updated":"2021-01-12T08:19:25Z","abstract":[{"lang":"eng","text":"Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis."}],"extern":"1","author":[{"first_name":"Sébastien","last_name":"Morin","full_name":"Morin, Sébastien"},{"first_name":"Troels E","last_name":"Linnet","full_name":"Linnet, Troels E"},{"first_name":"Mathilde","last_name":"Lescanne","full_name":"Lescanne, Mathilde"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul"},{"full_name":"Thompson, Gary S","first_name":"Gary S","last_name":"Thompson"},{"last_name":"Tollinger","first_name":"Martin","full_name":"Tollinger, Martin"},{"full_name":"Teilum, Kaare","last_name":"Teilum","first_name":"Kaare"},{"first_name":"Stéphane","last_name":"Gagné","full_name":"Gagné, Stéphane"},{"full_name":"Marion, Dominique","first_name":"Dominique","last_name":"Marion"},{"first_name":"Christian","last_name":"Griesinger","full_name":"Griesinger, Christian"},{"first_name":"Martin","last_name":"Blackledge","full_name":"Blackledge, Martin"},{"full_name":"d’Auvergne, Edward J","last_name":"d’Auvergne","first_name":"Edward J"}],"oa_version":"None","_id":"8459","page":"2219-2220","article_type":"original","date_created":"2020-09-18T10:08:07Z","doi":"10.1093/bioinformatics/btu166","status":"public","day":"01","type":"journal_article","title":"Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data","issue":"15","publication_identifier":{"issn":["1367-4803","1460-2059"]},"article_processing_charge":"No","quality_controlled":"1","publication":"Bioinformatics","month":"08","language":[{"iso":"eng"}],"publisher":"Oxford University Press","intvolume":"        30","date_published":"2014-08-01T00:00:00Z","citation":{"ista":"Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics. 30(15), 2219–2220.","apa":"Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>","short":"S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger, K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne, Bioinformatics 30 (2014) 2219–2220.","ieee":"S. Morin <i>et al.</i>, “Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data,” <i>Bioinformatics</i>, vol. 30, no. 15. Oxford University Press, pp. 2219–2220, 2014.","chicago":"Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/bioinformatics/btu166\">https://doi.org/10.1093/bioinformatics/btu166</a>.","ama":"Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. <i>Bioinformatics</i>. 2014;30(15):2219-2220. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>","mla":"Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” <i>Bioinformatics</i>, vol. 30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btu166\">10.1093/bioinformatics/btu166</a>."}},{"year":"2014","volume":53,"publication_status":"published","day":"18","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/anie.201311275","date_created":"2020-09-18T10:08:53Z","publication_identifier":{"issn":["1433-7851"]},"date_updated":"2021-01-12T08:19:25Z","title":"Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy","issue":"17","publisher":"Wiley","language":[{"iso":"eng"}],"month":"03","publication":"Angewandte Chemie International Edition","author":[{"last_name":"Ma","first_name":"Peixiang","full_name":"Ma, Peixiang"},{"first_name":"Jens D.","last_name":"Haller","full_name":"Haller, Jens D."},{"first_name":"Jérémy","last_name":"Zajakala","full_name":"Zajakala, Jérémy"},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"first_name":"Astrid C.","last_name":"Sivertsen","full_name":"Sivertsen, Astrid C."},{"first_name":"Dieter","last_name":"Willbold","full_name":"Willbold, Dieter"},{"first_name":"Jérôme","last_name":"Boisbouvier","full_name":"Boisbouvier, Jérôme"},{"first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"quality_controlled":"1","abstract":[{"text":"The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states.","lang":"eng"}],"extern":"1","article_processing_charge":"No","page":"4312-4317","article_type":"original","citation":{"mla":"Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>.","chicago":"Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen, Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” <i>Angewandte Chemie International Edition</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>.","ieee":"P. Ma <i>et al.</i>, “Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” <i>Angewandte Chemie International Edition</i>, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.","ama":"Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. 2014;53(17):4312-4317. doi:<a href=\"https://doi.org/10.1002/anie.201311275\">10.1002/anie.201311275</a>","short":"P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J. Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.","apa":"Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold, D., … Schanda, P. (2014). Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201311275\">https://doi.org/10.1002/anie.201311275</a>","ista":"Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition. 53(17), 4312–4317."},"date_published":"2014-03-18T00:00:00Z","intvolume":"        53","_id":"8460","oa_version":"None"},{"status":"public","doi":"10.1002/cpa.21509","date_created":"2020-09-18T10:47:01Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":67,"year":"2014","type":"journal_article","day":"01","publication_status":"published","date_updated":"2022-08-25T13:58:13Z","keyword":["Applied Mathematics","General Mathematics"],"title":"Arnol′d diffusion in a pendulum lattice","issue":"5","publication_identifier":{"issn":["0010-3640"]},"author":[{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","last_name":"Kaloshin"},{"full_name":"Levi, Mark","last_name":"Levi","first_name":"Mark"},{"last_name":"Saprykina","first_name":"Maria","full_name":"Saprykina, Maria"}],"publication":"Communications on Pure and Applied Mathematics","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way."}],"extern":"1","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Wiley","month":"05","intvolume":"        67","_id":"8500","oa_version":"None","page":"748-775","article_type":"original","date_published":"2014-05-01T00:00:00Z","citation":{"ista":"Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice. Communications on Pure and Applied Mathematics. 67(5), 748–775.","apa":"Kaloshin, V., Levi, M., &#38; Saprykina, M. (2014). Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>","short":"V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics 67 (2014) 748–775.","ama":"Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. <i>Communications on Pure and Applied Mathematics</i>. 2014;67(5):748-775. doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>","chicago":"Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2014. <a href=\"https://doi.org/10.1002/cpa.21509\">https://doi.org/10.1002/cpa.21509</a>.","ieee":"V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5. Wiley, pp. 748–775, 2014.","mla":"Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” <i>Communications on Pure and Applied Mathematics</i>, vol. 67, no. 5, Wiley, 2014, pp. 748–75, doi:<a href=\"https://doi.org/10.1002/cpa.21509\">10.1002/cpa.21509</a>."}},{"external_id":{"arxiv":["1304.3050"]},"author":[{"first_name":"Abed","last_name":"Bounemoura","full_name":"Bounemoura, Abed"},{"last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"}],"extern":"1","abstract":[{"text":"In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation.","lang":"eng"}],"_id":"8501","oa_version":"Preprint","page":"181-203","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","volume":14,"publication_status":"published","date_updated":"2021-01-12T08:19:43Z","keyword":["General Mathematics"],"publication":"Moscow Mathematical Journal","quality_controlled":"1","article_processing_charge":"No","publisher":"Independent University of Moscow","language":[{"iso":"eng"}],"month":"04","intvolume":"        14","citation":{"apa":"Bounemoura, A., &#38; Kaloshin, V. (2014). Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>","ista":"Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2), 181–203.","short":"A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.","chicago":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">https://doi.org/10.17323/1609-4514-2014-14-2-181-203</a>.","ieee":"A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.","ama":"Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom. <i>Moscow Mathematical Journal</i>. 2014;14(2):181-203. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>","mla":"Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of Non-Convex Hamiltonians with Two Degrees of Freedom.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-2-181-203\">10.17323/1609-4514-2014-14-2-181-203</a>."},"date_published":"2014-04-01T00:00:00Z","status":"public","arxiv":1,"doi":"10.17323/1609-4514-2014-14-2-181-203","date_created":"2020-09-18T10:47:09Z","type":"journal_article","day":"01","title":"Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom","issue":"2","publication_identifier":{"issn":["1609-3321","1609-4514"]}},{"abstract":[{"lang":"eng","text":"Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. "}],"extern":1,"quality_controlled":0,"author":[{"last_name":"Rosello","first_name":"Oriol","full_name":"Rosello, Oriol P"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"publication":"Genome Biology and Evolution","month":"08","publisher":"Oxford University Press","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"852","intvolume":"         6","date_published":"2014-08-01T00:00:00Z","citation":{"short":"O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.","ista":"Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.","apa":"Rosello, O., &#38; Kondrashov, F. (2014). Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>","mla":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>, vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>.","ieee":"O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein evolution after gene duplication,” <i>Genome Biology and Evolution</i>, vol. 6, no. 8. Oxford University Press, pp. 1949–1955, 2014.","chicago":"Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/gbe/evu159\">https://doi.org/10.1093/gbe/evu159</a>.","ama":"Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution after gene duplication. <i>Genome Biology and Evolution</i>. 2014;6(8):1949-1955. doi:<a href=\"https://doi.org/10.1093/gbe/evu159\">10.1093/gbe/evu159</a>"},"page":"1949 - 1955","doi":"10.1093/gbe/evu159","date_created":"2018-12-11T11:48:51Z","status":"public","type":"journal_article","day":"01","publication_status":"published","volume":6,"year":"2014","title":"Long-Term asymmetrical acceleration of protein evolution after gene duplication","issue":"8","date_updated":"2021-01-12T08:19:51Z","publist_id":"6797"},{"status":"public","date_created":"2018-12-11T11:48:52Z","doi":"10.1038/ncomms5868","year":"2014","acknowledgement":"K.P. acknowledges financial support from TRIPLE I and a Belspo mobility grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie Actions from the European Commission. Research in the lab of K.J.V. is supported by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme, KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR grant. The work of F.A.K. was supported by a grant of the HHMI International Early Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded by the European Regional Development Fund (ERDF), the European Union and the European Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral fellowship. Funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","volume":5,"publication_status":"published","day":"01","type":"journal_article","date_updated":"2021-01-12T08:20:01Z","title":"Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network","publist_id":"6790","publication":"Nature Communications","author":[{"last_name":"Pougach","first_name":"Ksenia","full_name":"Pougach, Ksenia S"},{"last_name":"Voet","first_name":"Arnout","full_name":"Voet, Arnout R"},{"first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Voordeckers, Karin","last_name":"Voordeckers","first_name":"Karin"},{"full_name":"Christiaens, Joaquin F","first_name":"Joaquin","last_name":"Christiaens"},{"full_name":"Baying, Bianka","last_name":"Baying","first_name":"Bianka"},{"full_name":"Bénès, Vladimı́r","first_name":"Vladimı́R","last_name":"Bénès"},{"last_name":"Sakai","first_name":"Ryo","full_name":"Sakai, Ryo"},{"full_name":"Aerts, Jan A","first_name":"Jan","last_name":"Aerts"},{"full_name":"Zhu, Bo","last_name":"Zhu","first_name":"Bo"},{"full_name":"Van Dijck, Patrick","last_name":"Van Dijck","first_name":"Patrick"},{"last_name":"Verstrepen","first_name":"Kevin","full_name":"Verstrepen, Kevin J"}],"quality_controlled":0,"abstract":[{"text":"The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network.","lang":"eng"}],"extern":1,"publisher":"Nature Publishing Group","month":"01","_id":"856","intvolume":"         5","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. Nature Communications. 5.","apa":"Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying, B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>","short":"K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying, V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications 5 (2014).","ieee":"K. Pougach <i>et al.</i>, “Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014.","chicago":"Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms5868\">https://doi.org/10.1038/ncomms5868</a>.","ama":"Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>","mla":"Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor Drives the Emergence of a New Regulatory Network.” <i>Nature Communications</i>, vol. 5, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms5868\">10.1038/ncomms5868</a>."},"date_published":"2014-01-01T00:00:00Z"},{"date_published":"2014-01-01T00:00:00Z","citation":{"short":"L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya, A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K. Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J. Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C. Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler, E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.","apa":"Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya, I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>","ista":"Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503), 109–114.","mla":"Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>, vol. 510, no. 7503, Nature Publishing Group, 2014, pp. 109–14, doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>.","ama":"Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary origins of neural systems. <i>Nature</i>. 2014;510(7503):109-114. doi:<a href=\"https://doi.org/10.1038/nature13400\">10.1038/nature13400</a>","ieee":"L. Moroz <i>et al.</i>, “The ctenophore genome and the evolutionary origins of neural systems,” <i>Nature</i>, vol. 510, no. 7503. Nature Publishing Group, pp. 109–114, 2014.","chicago":"Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian, Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the Evolutionary Origins of Neural Systems.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13400\">https://doi.org/10.1038/nature13400</a>."},"page":"109 - 114","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"intvolume":"       510","_id":"863","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"01","publisher":"Nature Publishing Group","extern":1,"abstract":[{"lang":"eng","text":"The origins of neural systems remain unresolved. In contrast to other basal metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived muscular systems. These holoplanktonic predators also have sophisticated ciliated locomotion, behaviour and distinct development. Here we present the draft genome of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore transcriptomes, and show that they are remarkably distinct from other animal genomes in their content of neurogenic, immune and developmental genes. Our integrative analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis is supported by comparative analysis of multiple gene families, including the apparent absence of HOX genes, canonical microRNA machinery, and reduced immune complement in ctenophores. Although two distinct nervous systems are well recognized in ctenophores, many bilaterian neuron-specific genes and genes of 'classical' neurotransmitter pathways either are absent or, if present, are not expressed in neurons. Our metabolomic and physiological data are consistent with the hypothesis that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals."}],"quality_controlled":0,"author":[{"first_name":"Leonid","last_name":"Moroz","full_name":"Moroz, Leonid L"},{"full_name":"Kocot, Kevin M","first_name":"Kevin","last_name":"Kocot"},{"full_name":"Citarella, Mathew R","last_name":"Citarella","first_name":"Mathew"},{"first_name":"Sohn","last_name":"Dosung","full_name":"Dosung, Sohn"},{"first_name":"Tigran","last_name":"Norekian","full_name":"Norekian, Tigran P"},{"first_name":"Inna","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna"},{"first_name":"Anastasia","last_name":"Grigorenko","full_name":"Grigorenko, Anastasia P"},{"full_name":"Dailey, Christopher A","last_name":"Dailey","first_name":"Christopher"},{"first_name":"Eugene","last_name":"Berezikov","full_name":"Berezikov, Eugene"},{"first_name":"Katherine","last_name":"Buckley","full_name":"Buckley, Katherine M"},{"first_name":"Andrey","last_name":"Ptitsyn","full_name":"Ptitsyn, Andrey A"},{"full_name":"Reshetov, Denis A","last_name":"Reshetov","first_name":"Denis"},{"full_name":"Mukherjee, Krishanu","last_name":"Mukherjee","first_name":"Krishanu"},{"first_name":"Tatiana","last_name":"Moroz","full_name":"Moroz, Tatiana P"},{"first_name":"Yelena","last_name":"Bobkova","full_name":"Bobkova, Yelena V"},{"last_name":"Yu","first_name":"Fahong","full_name":"Yu, Fahong"},{"last_name":"Kapitonov","first_name":"Vladimir","full_name":"Kapitonov, Vladimir V"},{"first_name":"Jerzy","last_name":"Jurka","full_name":"Jurka, Jerzy W"},{"first_name":"Yuriy","last_name":"Bobkov","full_name":"Bobkov, Yuriy V"},{"last_name":"Swore","first_name":"Joshua","full_name":"Swore, Joshua J"},{"full_name":"Girardo, David O","first_name":"David","last_name":"Girardo"},{"last_name":"Fodor","first_name":"Alexander","full_name":"Fodor, Alexander"},{"last_name":"Gusev","first_name":"Fedor","full_name":"Gusev, Fedor E"},{"full_name":"Sanford, Rachel S","first_name":"Rachel","last_name":"Sanford"},{"full_name":"Bruders, Rebecca","first_name":"Rebecca","last_name":"Bruders"},{"full_name":"Kittler, Ellen L","last_name":"Kittler","first_name":"Ellen"},{"full_name":"Mills, Claudia E","first_name":"Claudia","last_name":"Mills"},{"first_name":"Jonathan","last_name":"Rast","full_name":"Rast, Jonathan P"},{"last_name":"Derelle","first_name":"Romain","full_name":"Derelle, Romain"},{"last_name":"Solovyev","first_name":"Victor","full_name":"Solovyev, Victor"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Billie","last_name":"Swalla","full_name":"Swalla, Billie J"},{"full_name":"Sweedler, Jonathan V","last_name":"Sweedler","first_name":"Jonathan"},{"first_name":"Evgeny","last_name":"Rogaev","full_name":"Rogaev, Evgeny I"},{"full_name":"Halanych, Kenneth M","last_name":"Halanych","first_name":"Kenneth"},{"last_name":"Kohn","first_name":"Andrea","full_name":"Kohn, Andrea B"}],"publication":"Nature","publist_id":"6785","title":"The ctenophore genome and the evolutionary origins of neural systems","issue":"7503","date_updated":"2021-01-12T08:20:21Z","day":"01","type":"journal_article","publication_status":"published","acknowledgement":"We thank Friday Harbor Laboratories for facilities during animal collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters, J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ, RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank F. Nivens for videos and P. L. Williams for database support. This work was supported by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH (1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310 to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H., L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033 (Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424), EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology Program 117 and Molette laboratory 22.","year":"2014","volume":510,"doi":"10.1038/nature13400","date_created":"2018-12-11T11:48:54Z","status":"public"},{"publist_id":"6782","title":"Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling","issue":"4","date_updated":"2021-01-12T08:20:24Z","type":"journal_article","day":"15","publication_status":"published","year":"2014","volume":87,"doi":"10.1016/j.bcp.2013.12.007","date_created":"2018-12-11T11:48:55Z","status":"public","date_published":"2014-02-15T00:00:00Z","citation":{"ama":"Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. 2014;87(4):571-578. doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>","chicago":"Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov, J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>.","ieee":"A. Koval <i>et al.</i>, “Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling,” <i>Biochemical Pharmacology</i>, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.","mla":"Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” <i>Biochemical Pharmacology</i>, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:<a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">10.1016/j.bcp.2013.12.007</a>.","ista":"Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. Biochemical Pharmacology. 87(4), 571–578.","apa":"Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko, J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer cells via inhibition of canonical Wnt signaling. <i>Biochemical Pharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bcp.2013.12.007\">https://doi.org/10.1016/j.bcp.2013.12.007</a>","short":"A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko, A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578."},"page":"571 - 578","intvolume":"        87","_id":"865","month":"02","publisher":"Elsevier","abstract":[{"lang":"eng","text":"Research on existing drugs often discovers novel mechanisms of their action and leads to the expansion of their therapeutic scope and subsequent remarketing. The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays critical roles in cancer development and progression. However, drugs which disrupt this pathway are unavailable despite the high demand. Here we report an attempt to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved drugs. We performed an in silico screening which brought up several potential antagonists of the ligand-receptor interaction. 14 of these substances were tested using the TopFlash luciferase reporter assay and four of them identified as active and specific inhibitors of the Wnt3a-induced signaling. However, further analysis through GTP-binding and β-catenin stabilization assays showed that the compounds do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels. We further describe the previously unknown inhibitory activity of an anti-leprosy drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These data provide a basis for further investigations of the efficiency of clofazimine in treatment of Wnt-dependent cancers."}],"extern":1,"quality_controlled":0,"author":[{"last_name":"Koval","first_name":"Alexey","full_name":"Koval, Alexey V"},{"first_name":"Peter","last_name":"Vlasov","full_name":"Vlasov, Peter K"},{"full_name":"Shichkova, Polina","last_name":"Shichkova","first_name":"Polina"},{"first_name":"S","last_name":"Khunderyakova","full_name":"Khunderyakova, S"},{"last_name":"Markov","first_name":"Yury","full_name":"Markov, Yury"},{"full_name":"Panchenko, J","last_name":"Panchenko","first_name":"J"},{"full_name":"Volodina, A","first_name":"A","last_name":"Volodina"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Katanaev","first_name":"Vladimir","full_name":"Katanaev, Vladimir L"}],"publication":"Biochemical Pharmacology"},{"date_updated":"2025-08-05T14:53:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","volume":26,"year":"2014","oa_version":"None","_id":"892","oa":1,"page":"104 - 112","abstract":[{"lang":"eng","text":"The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution."}],"extern":"1","author":[{"last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"},{"full_name":"Finkelstein, Alexei","first_name":"Alexei","last_name":"Finkelstein"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"}],"title":"A structural perspective of compensatory evolution","publist_id":"6756","date_created":"2018-12-11T11:49:03Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.sbi.2014.05.004"}],"doi":"10.1016/j.sbi.2014.05.004","status":"public","day":"01","type":"journal_article","acknowledgement":"The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.\r\n","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"intvolume":"        26","date_published":"2014-06-01T00:00:00Z","citation":{"ama":"Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. 2014;26:104-112. doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>","chicago":"Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>.","ieee":"D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of compensatory evolution,” <i>Current Opinion in Structural Biology</i>, vol. 26. Elsevier, pp. 104–112, 2014.","mla":"Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.” <i>Current Opinion in Structural Biology</i>, vol. 26, Elsevier, 2014, pp. 104–12, doi:<a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">10.1016/j.sbi.2014.05.004</a>.","ista":"Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of compensatory evolution. Current Opinion in Structural Biology. 26, 104–112.","apa":"Ivankov, D., Finkelstein, A., &#38; Kondrashov, F. (2014). A structural perspective of compensatory evolution. <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2014.05.004\">https://doi.org/10.1016/j.sbi.2014.05.004</a>","short":"D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural Biology 26 (2014) 104–112."},"article_processing_charge":"No","publication":"Current Opinion in Structural Biology","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","month":"06","language":[{"iso":"eng"}],"publisher":"Elsevier"},{"date_updated":"2023-02-23T13:47:35Z","keyword":["General Chemistry","Condensed Matter Physics"],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","volume":10,"year":"2014","publication_status":"published","_id":"9050","oa_version":"Preprint","article_type":"original","oa":1,"external_id":{"arxiv":["1309.5662"],"pmid":["24800268"]},"author":[{"full_name":"Takagi, Daisuke","last_name":"Takagi","first_name":"Daisuke"},{"orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci"},{"first_name":"Adam B.","last_name":"Braunschweig","full_name":"Braunschweig, Adam B."},{"full_name":"Shelley, Michael J.","last_name":"Shelley","first_name":"Michael J."},{"full_name":"Zhang, Jun","first_name":"Jun","last_name":"Zhang"}],"abstract":[{"text":"Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter.","lang":"eng"}],"extern":"1","issue":"11","title":"Hydrodynamic capture of microswimmers into sphere-bound orbits","scopus_import":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1309.5662","open_access":"1"}],"doi":"10.1039/c3sm52815d","arxiv":1,"date_created":"2021-02-01T13:43:31Z","day":"21","type":"journal_article","intvolume":"        10","article_number":"1784","citation":{"mla":"Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>, vol. 10, no. 11, 1784, Royal Society of Chemistry , 2014, doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>.","ama":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. 2014;10(11). doi:<a href=\"https://doi.org/10.1039/c3sm52815d\">10.1039/c3sm52815d</a>","chicago":"Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley, and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.” <i>Soft Matter</i>. Royal Society of Chemistry , 2014. <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>.","ieee":"D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang, “Hydrodynamic capture of microswimmers into sphere-bound orbits,” <i>Soft Matter</i>, vol. 10, no. 11. Royal Society of Chemistry , 2014.","short":"D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft Matter 10 (2014).","apa":"Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., &#38; Zhang, J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c3sm52815d\">https://doi.org/10.1039/c3sm52815d</a>","ista":"Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784."},"date_published":"2014-03-21T00:00:00Z","publication":"Soft Matter","quality_controlled":"1","article_processing_charge":"No","publisher":"Royal Society of Chemistry ","language":[{"iso":"eng"}],"month":"03","pmid":1}]