[{"main_file_link":[{"url":"https://arxiv.org/abs/2004.14599","open_access":"1"}],"publisher":"American Chemical Society","department":[{"_id":"NanoFab"}],"publication":"Nano Letters","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"citation":{"short":"J. Duan, N. Capote-Robayna, J. Taboada-Gutiérrez, G. Álvarez-Pérez, I. Prieto Gonzalez, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Nano Letters 20 (2020) 5323–5329.","ista":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, Álvarez-Pérez G, Prieto Gonzalez I, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2020. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. Nano Letters. 20(7), 5323–5329.","chicago":"Duan, Jiahua, Nathaniel Capote-Robayna, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Ivan Prieto Gonzalez, Javier Martín-Sánchez, Alexey Y. Nikitin, and Pablo Alonso-González. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>.","ama":"Duan J, Capote-Robayna N, Taboada-Gutiérrez J, et al. Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. 2020;20(7):5323-5329. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>","mla":"Duan, Jiahua, et al. “Twisted Nano-Optics: Manipulating Light at the Nanoscale with Twisted Phonon Polaritonic Slabs.” <i>Nano Letters</i>, vol. 20, no. 7, American Chemical Society, 2020, pp. 5323–29, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">10.1021/acs.nanolett.0c01673</a>.","apa":"Duan, J., Capote-Robayna, N., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Prieto Gonzalez, I., Martín-Sánchez, J., … Alonso-González, P. (2020). Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c01673\">https://doi.org/10.1021/acs.nanolett.0c01673</a>","ieee":"J. Duan <i>et al.</i>, “Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs,” <i>Nano Letters</i>, vol. 20, no. 7. American Chemical Society, pp. 5323–5329, 2020."},"title":"Twisted nano-optics: Manipulating light at the nanoscale with twisted phonon polaritonic slabs","_id":"10866","date_updated":"2023-09-05T12:05:58Z","day":"01","status":"public","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"doi":"10.1021/acs.nanolett.0c01673","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","page":"5323-5329","arxiv":1,"article_processing_charge":"No","type":"journal_article","intvolume":"        20","language":[{"iso":"eng"}],"acknowledgement":"J.T.-G. and G.Á.-P. acknowledge support through the Severo Ochoa Program from the\r\nGovernment of the Principality of Asturias (nos. PA-18-PF-BP17-126 and PA20-PF-BP19-053,\r\nrespectively). J. M-S acknowledges financial support through the Ramón y Cajal Program from\r\nthe Government of Spain (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of\r\nScience, Innovation and Universities (national project no. MAT201788358-C3-3-R). P.A.-G.\r\nacknowledges support from the European Research Council under starting grant no. 715496,\r\n2DNANOPTICA.","isi":1,"oa":1,"issue":"7","date_created":"2022-03-18T11:37:38Z","date_published":"2020-07-01T00:00:00Z","article_type":"original","year":"2020","volume":20,"month":"07","abstract":[{"lang":"eng","text":"Recent discoveries have shown that, when two layers of van der Waals (vdW) materials are superimposed with a relative twist angle between them, the electronic properties of the coupled system can be dramatically altered. Here, we demonstrate that a similar concept can be extended to the optics realm, particularly to propagating phonon polaritons–hybrid light-matter interactions. To do this, we fabricate stacks composed of two twisted slabs of a vdW crystal (α-MoO3) supporting anisotropic phonon polaritons (PhPs), and image the propagation of the latter when launched by localized sources. Our images reveal that, under a critical angle, the PhPs isofrequency curve undergoes a topological transition, in which the propagation of PhPs is strongly guided (canalization regime) along predetermined directions without geometric spreading. These results demonstrate a new degree of freedom (twist angle) for controlling the propagation of polaritons at the nanoscale with potential for nanoimaging, (bio)-sensing, or heat management."}],"author":[{"full_name":"Duan, Jiahua","last_name":"Duan","first_name":"Jiahua"},{"last_name":"Capote-Robayna","first_name":"Nathaniel","full_name":"Capote-Robayna, Nathaniel"},{"full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez","first_name":"Javier"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"publication_status":"published","pmid":1,"external_id":{"isi":["000548893200082"],"pmid":["32530634"],"arxiv":["2004.14599"]}},{"language":[{"iso":"eng"}],"oa":1,"issue":"11","intvolume":"        53","date_published":"2020-11-17T00:00:00Z","year":"2020","article_type":"original","date_created":"2023-08-01T09:35:50Z","volume":53,"abstract":[{"text":"In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication.\r\n\r\nIn this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior.\r\n\r\nAlthough we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account.","lang":"eng"}],"month":"11","author":[{"last_name":"Grommet","first_name":"Angela B.","full_name":"Grommet, Angela B."},{"full_name":"Lee, Lucia M.","last_name":"Lee","first_name":"Lucia M."},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["32969638"]},"publication_status":"published","pmid":1,"publication":"Accounts of Chemical Research","citation":{"ama":"Grommet AB, Lee LM, Klajn R. Molecular photoswitching in confined spaces. <i>Accounts of Chemical Research</i>. 2020;53(11):2600-2610. doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">10.1021/acs.accounts.0c00434</a>","apa":"Grommet, A. B., Lee, L. M., &#38; Klajn, R. (2020). Molecular photoswitching in confined spaces. <i>Accounts of Chemical Research</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">https://doi.org/10.1021/acs.accounts.0c00434</a>","mla":"Grommet, Angela B., et al. “Molecular Photoswitching in Confined Spaces.” <i>Accounts of Chemical Research</i>, vol. 53, no. 11, American Chemical Society, 2020, pp. 2600–10, doi:<a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">10.1021/acs.accounts.0c00434</a>.","ieee":"A. B. Grommet, L. M. Lee, and R. Klajn, “Molecular photoswitching in confined spaces,” <i>Accounts of Chemical Research</i>, vol. 53, no. 11. American Chemical Society, pp. 2600–2610, 2020.","short":"A.B. Grommet, L.M. Lee, R. Klajn, Accounts of Chemical Research 53 (2020) 2600–2610.","ista":"Grommet AB, Lee LM, Klajn R. 2020. Molecular photoswitching in confined spaces. Accounts of Chemical Research. 53(11), 2600–2610.","chicago":"Grommet, Angela B., Lucia M. Lee, and Rafal Klajn. “Molecular Photoswitching in Confined Spaces.” <i>Accounts of Chemical Research</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.accounts.0c00434\">https://doi.org/10.1021/acs.accounts.0c00434</a>."},"keyword":["General Medicine","General Chemistry"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acs.accounts.0c00434"}],"publisher":"American Chemical Society","title":"Molecular photoswitching in confined spaces","_id":"13361","date_updated":"2024-10-14T12:12:31Z","day":"17","publication_identifier":{"eissn":["1520-4898"],"issn":["0001-4842"]},"doi":"10.1021/acs.accounts.0c00434","quality_controlled":"1","status":"public","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2600-2610","type":"journal_article","extern":"1","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments."}],"month":"10","volume":142,"article_type":"original","year":"2020","date_published":"2020-10-04T00:00:00Z","date_created":"2023-08-01T09:36:10Z","issue":"41","oa":1,"language":[{"iso":"eng"}],"intvolume":"       142","external_id":{"pmid":["33006898"]},"pmid":1,"publication_status":"published","author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"last_name":"Ahrens","first_name":"Johannes","full_name":"Ahrens, Johannes"},{"full_name":"Shimon, Linda J. W.","first_name":"Linda J. W.","last_name":"Shimon"},{"first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"day":"04","date_updated":"2024-10-14T12:12:41Z","title":"Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage","_id":"13362","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"citation":{"short":"J. Gemen, J. Ahrens, L.J.W. Shimon, R. Klajn, Journal of the American Chemical Society 142 (2020) 17721–17729.","ista":"Gemen J, Ahrens J, Shimon LJW, Klajn R. 2020. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. Journal of the American Chemical Society. 142(41), 17721–17729.","chicago":"Gemen, Julius, Johannes Ahrens, Linda J. W. Shimon, and Rafal Klajn. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c08589\">https://doi.org/10.1021/jacs.0c08589</a>.","ama":"Gemen J, Ahrens J, Shimon LJW, Klajn R. Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(41):17721-17729. doi:<a href=\"https://doi.org/10.1021/jacs.0c08589\">10.1021/jacs.0c08589</a>","mla":"Gemen, Julius, et al. “Modulating the Optical Properties of BODIPY Dyes by Noncovalent Dimerization within a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 41, American Chemical Society, 2020, pp. 17721–29, doi:<a href=\"https://doi.org/10.1021/jacs.0c08589\">10.1021/jacs.0c08589</a>.","apa":"Gemen, J., Ahrens, J., Shimon, L. J. W., &#38; Klajn, R. (2020). Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c08589\">https://doi.org/10.1021/jacs.0c08589</a>","ieee":"J. Gemen, J. Ahrens, L. J. W. Shimon, and R. Klajn, “Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 41. American Chemical Society, pp. 17721–17729, 2020."},"publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.0c08589"}],"type":"journal_article","extern":"1","article_processing_charge":"No","page":"17721-17729","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","doi":"10.1021/jacs.0c08589","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"status":"public"},{"day":"11","date_updated":"2023-08-07T10:11:41Z","title":"Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors","_id":"13363","keyword":["Biomaterials","Biotechnology","General Materials Science","General Chemistry"],"citation":{"chicago":"Moreno, Silvia, Priyanka Sharan, Johanna Engelke, Hannes Gumz, Susanne Boye, Ulrich Oertel, Peng Wang, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” <i>Small</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/smll.202002135\">https://doi.org/10.1002/smll.202002135</a>.","ista":"Moreno S, Sharan P, Engelke J, Gumz H, Boye S, Oertel U, Wang P, Banerjee S, Klajn R, Voit B, Lederer A, Appelhans D. 2020. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. Small. 16(37), 2002135.","short":"S. Moreno, P. Sharan, J. Engelke, H. Gumz, S. Boye, U. Oertel, P. Wang, S. Banerjee, R. Klajn, B. Voit, A. Lederer, D. Appelhans, Small 16 (2020).","ieee":"S. Moreno <i>et al.</i>, “Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors,” <i>Small</i>, vol. 16, no. 37. Wiley, 2020.","mla":"Moreno, Silvia, et al. “Light‐driven Proton Transfer for Cyclic and Temporal Switching of Enzymatic Nanoreactors.” <i>Small</i>, vol. 16, no. 37, 2002135, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/smll.202002135\">10.1002/smll.202002135</a>.","apa":"Moreno, S., Sharan, P., Engelke, J., Gumz, H., Boye, S., Oertel, U., … Appelhans, D. (2020). Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. <i>Small</i>. Wiley. <a href=\"https://doi.org/10.1002/smll.202002135\">https://doi.org/10.1002/smll.202002135</a>","ama":"Moreno S, Sharan P, Engelke J, et al. Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors. <i>Small</i>. 2020;16(37). doi:<a href=\"https://doi.org/10.1002/smll.202002135\">10.1002/smll.202002135</a>"},"publication":"Small","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/smll.202002135"}],"extern":"1","type":"journal_article","article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","publication_identifier":{"issn":["1613-6810"],"eissn":["1613-6829"]},"doi":"10.1002/smll.202002135","status":"public","abstract":[{"lang":"eng","text":"Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand."}],"month":"08","volume":16,"year":"2020","article_type":"original","date_published":"2020-08-11T00:00:00Z","date_created":"2023-08-01T09:36:48Z","oa":1,"issue":"37","language":[{"iso":"eng"}],"intvolume":"        16","external_id":{"pmid":["32783385"]},"pmid":1,"article_number":"2002135","publication_status":"published","author":[{"first_name":"Silvia","last_name":"Moreno","full_name":"Moreno, Silvia"},{"full_name":"Sharan, Priyanka","first_name":"Priyanka","last_name":"Sharan"},{"full_name":"Engelke, Johanna","last_name":"Engelke","first_name":"Johanna"},{"full_name":"Gumz, Hannes","last_name":"Gumz","first_name":"Hannes"},{"last_name":"Boye","first_name":"Susanne","full_name":"Boye, Susanne"},{"first_name":"Ulrich","last_name":"Oertel","full_name":"Oertel, Ulrich"},{"first_name":"Peng","last_name":"Wang","full_name":"Wang, Peng"},{"full_name":"Banerjee, Susanta","last_name":"Banerjee","first_name":"Susanta"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"},{"full_name":"Voit, Brigitte","last_name":"Voit","first_name":"Brigitte"},{"full_name":"Lederer, Albena","first_name":"Albena","last_name":"Lederer"},{"full_name":"Appelhans, Dietmar","first_name":"Dietmar","last_name":"Appelhans"}]},{"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","page":"14557-14565","status":"public","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"doi":"10.1021/jacs.0c06146","quality_controlled":"1","article_processing_charge":"No","type":"journal_article","extern":"1","_id":"13364","title":"Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/jacs.0c06146"}],"publisher":"American Chemical Society","publication":"Journal of the American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"citation":{"apa":"Canton, M., Grommet, A. B., Pesce, L., Gemen, J., Li, S., Diskin-Posner, Y., … Klajn, R. (2020). Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c06146\">https://doi.org/10.1021/jacs.0c06146</a>","mla":"Canton, Martina, et al. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 34, American Chemical Society, 2020, pp. 14557–65, doi:<a href=\"https://doi.org/10.1021/jacs.0c06146\">10.1021/jacs.0c06146</a>.","ieee":"M. Canton <i>et al.</i>, “Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 34. American Chemical Society, pp. 14557–14565, 2020.","ama":"Canton M, Grommet AB, Pesce L, et al. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(34):14557-14565. doi:<a href=\"https://doi.org/10.1021/jacs.0c06146\">10.1021/jacs.0c06146</a>","ista":"Canton M, Grommet AB, Pesce L, Gemen J, Li S, Diskin-Posner Y, Credi A, Pavan GM, Andréasson J, Klajn R. 2020. Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage. Journal of the American Chemical Society. 142(34), 14557–14565.","chicago":"Canton, Martina, Angela B. Grommet, Luca Pesce, Julius Gemen, Shiming Li, Yael Diskin-Posner, Alberto Credi, Giovanni M. Pavan, Joakim Andréasson, and Rafal Klajn. “Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c06146\">https://doi.org/10.1021/jacs.0c06146</a>.","short":"M. Canton, A.B. Grommet, L. Pesce, J. Gemen, S. Li, Y. Diskin-Posner, A. Credi, G.M. Pavan, J. Andréasson, R. Klajn, Journal of the American Chemical Society 142 (2020) 14557–14565."},"day":"14","date_updated":"2023-08-07T10:15:38Z","publication_status":"published","pmid":1,"external_id":{"pmid":["32791832"]},"author":[{"full_name":"Canton, Martina","last_name":"Canton","first_name":"Martina"},{"full_name":"Grommet, Angela B.","first_name":"Angela B.","last_name":"Grommet"},{"full_name":"Pesce, Luca","last_name":"Pesce","first_name":"Luca"},{"first_name":"Julius","last_name":"Gemen","full_name":"Gemen, Julius"},{"full_name":"Li, Shiming","first_name":"Shiming","last_name":"Li"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"last_name":"Credi","first_name":"Alberto","full_name":"Credi, Alberto"},{"full_name":"Pavan, Giovanni M.","last_name":"Pavan","first_name":"Giovanni M."},{"full_name":"Andréasson, Joakim","last_name":"Andréasson","first_name":"Joakim"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"date_created":"2023-08-01T09:36:59Z","date_published":"2020-08-14T00:00:00Z","article_type":"original","year":"2020","intvolume":"       142","language":[{"iso":"eng"}],"issue":"34","oa":1,"month":"08","abstract":[{"lang":"eng","text":"Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions."}],"volume":142},{"day":"30","date_updated":"2023-08-07T10:18:53Z","_id":"13365","title":"Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage","main_file_link":[{"url":"https://doi.org/10.1021/jacs.0c03444","open_access":"1"}],"publisher":"American Chemical Society","publication":"Journal of the American Chemical Society","citation":{"mla":"Pesce, Luca, et al. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>, vol. 142, no. 21, American Chemical Society, 2020, pp. 9792–802, doi:<a href=\"https://doi.org/10.1021/jacs.0c03444\">10.1021/jacs.0c03444</a>.","apa":"Pesce, L., Perego, C., Grommet, A. B., Klajn, R., &#38; Pavan, G. M. (2020). Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.0c03444\">https://doi.org/10.1021/jacs.0c03444</a>","ieee":"L. Pesce, C. Perego, A. B. Grommet, R. Klajn, and G. M. Pavan, “Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage,” <i>Journal of the American Chemical Society</i>, vol. 142, no. 21. American Chemical Society, pp. 9792–9802, 2020.","ama":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. <i>Journal of the American Chemical Society</i>. 2020;142(21):9792-9802. doi:<a href=\"https://doi.org/10.1021/jacs.0c03444\">10.1021/jacs.0c03444</a>","ista":"Pesce L, Perego C, Grommet AB, Klajn R, Pavan GM. 2020. Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage. Journal of the American Chemical Society. 142(21), 9792–9802.","chicago":"Pesce, Luca, Claudio Perego, Angela B. Grommet, Rafal Klajn, and Giovanni M. Pavan. “Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/jacs.0c03444\">https://doi.org/10.1021/jacs.0c03444</a>.","short":"L. Pesce, C. Perego, A.B. Grommet, R. Klajn, G.M. Pavan, Journal of the American Chemical Society 142 (2020) 9792–9802."},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"article_processing_charge":"No","extern":"1","type":"journal_article","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"9792-9802","status":"public","doi":"10.1021/jacs.0c03444","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"quality_controlled":"1","month":"04","abstract":[{"lang":"eng","text":"Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions."}],"volume":142,"date_created":"2023-08-01T09:37:12Z","date_published":"2020-04-30T00:00:00Z","article_type":"original","year":"2020","intvolume":"       142","oa":1,"issue":"21","language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"external_id":{"pmid":["32353237"]},"author":[{"last_name":"Pesce","first_name":"Luca","full_name":"Pesce, Luca"},{"first_name":"Claudio","last_name":"Perego","full_name":"Perego, Claudio"},{"full_name":"Grommet, Angela B.","last_name":"Grommet","first_name":"Angela B."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"},{"first_name":"Giovanni M.","last_name":"Pavan","full_name":"Pavan, Giovanni M."}]},{"language":[{"iso":"eng"}],"oa":1,"intvolume":"        11","date_published":"2020-11-23T00:00:00Z","article_type":"original","year":"2020","date_created":"2024-03-20T10:43:07Z","volume":11,"abstract":[{"lang":"eng","text":"Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the <jats:italic>Desulfovibrio vulgaris</jats:italic> type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool."}],"month":"11","author":[{"full_name":"O’Brien, Roisin E.","first_name":"Roisin E.","last_name":"O’Brien"},{"first_name":"Inês C.","last_name":"Santos","full_name":"Santos, Inês C."},{"full_name":"Wrapp, Daniel","last_name":"Wrapp","first_name":"Daniel"},{"first_name":"Jack Peter Kelly","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"full_name":"Schwartz, Evan A.","first_name":"Evan A.","last_name":"Schwartz"},{"last_name":"Brodbelt","first_name":"Jennifer S.","full_name":"Brodbelt, Jennifer S."},{"full_name":"Taylor, David W.","first_name":"David W.","last_name":"Taylor"}],"external_id":{"pmid":["33230133"]},"publication_status":"published","article_number":"5931","pmid":1,"publication":"Nature Communications","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"citation":{"ama":"O’Brien RE, Santos IC, Wrapp D, et al. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19785-8\">10.1038/s41467-020-19785-8</a>","apa":"O’Brien, R. E., Santos, I. C., Wrapp, D., Bravo, J. P. K., Schwartz, E. A., Brodbelt, J. S., &#38; Taylor, D. W. (2020). Structural basis for assembly of non-canonical small subunits into type I-C Cascade. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19785-8\">https://doi.org/10.1038/s41467-020-19785-8</a>","mla":"O’Brien, Roisin E., et al. “Structural Basis for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” <i>Nature Communications</i>, vol. 11, 5931, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19785-8\">10.1038/s41467-020-19785-8</a>.","ieee":"R. E. O’Brien <i>et al.</i>, “Structural basis for assembly of non-canonical small subunits into type I-C Cascade,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","short":"R.E. O’Brien, I.C. Santos, D. Wrapp, J.P.K. Bravo, E.A. Schwartz, J.S. Brodbelt, D.W. Taylor, Nature Communications 11 (2020).","ista":"O’Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW. 2020. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nature Communications. 11, 5931.","chicago":"O’Brien, Roisin E., Inês C. Santos, Daniel Wrapp, Jack Peter Kelly Bravo, Evan A. Schwartz, Jennifer S. Brodbelt, and David W. Taylor. “Structural Basis for Assembly of Non-Canonical Small Subunits into Type I-C Cascade.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19785-8\">https://doi.org/10.1038/s41467-020-19785-8</a>."},"main_file_link":[{"url":"https://doi.org/10.1038/s41467-020-19785-8","open_access":"1"}],"publisher":"Springer Nature","_id":"15142","title":"Structural basis for assembly of non-canonical small subunits into type I-C Cascade","date_updated":"2024-06-04T05:52:51Z","day":"23","doi":"10.1038/s41467-020-19785-8","publication_identifier":{"issn":["2041-1723"]},"quality_controlled":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","extern":"1","type":"journal_article","article_processing_charge":"Yes"},{"article_processing_charge":"No","type":"journal_article","extern":"1","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","oa_version":"Published Version","scopus_import":"1","page":"10628-10639","status":"public","publication_identifier":{"issn":["1744-683X","1744-6848"]},"doi":"10.1039/d0sm00712a","quality_controlled":"1","day":"06","OA_type":"hybrid","date_updated":"2024-10-16T12:53:17Z","_id":"10341","title":"Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes","OA_place":"publisher","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.05.01.071761v1","open_access":"1"}],"publisher":"Royal Society of Chemistry","publication":"Soft Matter","citation":{"chicago":"Debets, V. E., L. M. C. Janssen, and Anđela Šarić. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>.","ista":"Debets VE, Janssen LMC, Šarić A. 2020. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter. 16(47), 10628–10639.","short":"V.E. Debets, L.M.C. Janssen, A. Šarić, Soft Matter 16 (2020) 10628–10639.","ieee":"V. E. Debets, L. M. C. Janssen, and A. Šarić, “Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes,” <i>Soft Matter</i>, vol. 16, no. 47. Royal Society of Chemistry, pp. 10628–10639, 2020.","apa":"Debets, V. E., Janssen, L. M. C., &#38; Šarić, A. (2020). Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm00712a\">https://doi.org/10.1039/d0sm00712a</a>","mla":"Debets, V. E., et al. “Characterising the Diffusion of Biological Nanoparticles on Fluid and Cross-Linked Membranes.” <i>Soft Matter</i>, vol. 16, no. 47, Royal Society of Chemistry, 2020, pp. 10628–39, doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>.","ama":"Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. <i>Soft Matter</i>. 2020;16(47):10628-10639. doi:<a href=\"https://doi.org/10.1039/d0sm00712a\">10.1039/d0sm00712a</a>"},"keyword":["condensed matter physics","general chemistry"],"publication_status":"published","pmid":1,"external_id":{"pmid":["33084724"]},"author":[{"last_name":"Debets","first_name":"V. E.","full_name":"Debets, V. E."},{"first_name":"L. M. C.","last_name":"Janssen","full_name":"Janssen, L. M. C."},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"month":"10","abstract":[{"text":"Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.","lang":"eng"}],"volume":16,"date_created":"2021-11-26T06:29:41Z","date_published":"2020-10-06T00:00:00Z","article_type":"original","year":"2020","intvolume":"        16","oa":1,"issue":"47","language":[{"iso":"eng"}],"acknowledgement":"We thank Jessica McQuade for her input at the start of the project. We acknowledge support from the ERASMUS Placement Programme (V. E. D.), the UCL Institute for the Physics of Living Systems (V. E. D. and A. Š.), the UCL Global Engagement Fund (L. M. C. J.), and the Royal Society (A. Š.)."},{"_id":"10350","title":"Identification of on- and off-pathway oligomers in amyloid fibril formation","keyword":["general chemistry"],"citation":{"chicago":"Dear, Alexander J., Georg Meisl, Anđela Šarić, Thomas C. T. Michaels, Magnus Kjaergaard, Sara Linse, and Tuomas P. J. Knowles. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>.","ista":"Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. 2020. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chemical Science. 11(24), 6236–6247.","short":"A.J. Dear, G. Meisl, A. Šarić, T.C.T. Michaels, M. Kjaergaard, S. Linse, T.P.J. Knowles, Chemical Science 11 (2020) 6236–6247.","ieee":"A. J. Dear <i>et al.</i>, “Identification of on- and off-pathway oligomers in amyloid fibril formation,” <i>Chemical Science</i>, vol. 11, no. 24. Royal Society of Chemistry, pp. 6236–6247, 2020.","mla":"Dear, Alexander J., et al. “Identification of On- and off-Pathway Oligomers in Amyloid Fibril Formation.” <i>Chemical Science</i>, vol. 11, no. 24, Royal Society of Chemistry, 2020, pp. 6236–47, doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>.","apa":"Dear, A. J., Meisl, G., Šarić, A., Michaels, T. C. T., Kjaergaard, M., Linse, S., &#38; Knowles, T. P. J. (2020). Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c9sc06501f\">https://doi.org/10.1039/c9sc06501f</a>","ama":"Dear AJ, Meisl G, Šarić A, et al. Identification of on- and off-pathway oligomers in amyloid fibril formation. <i>Chemical Science</i>. 2020;11(24):6236-6247. doi:<a href=\"https://doi.org/10.1039/c9sc06501f\">10.1039/c9sc06501f</a>"},"publication":"Chemical Science","publisher":"Royal Society of Chemistry","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2020/sc/c9sc06501f","open_access":"1"}],"day":"08","date_updated":"2021-11-26T11:21:20Z","page":"6236-6247","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","publication_identifier":{"issn":["2041-6520"],"eissn":["2041-6539"]},"doi":"10.1039/c9sc06501f","status":"public","extern":"1","type":"journal_article","article_processing_charge":"No","year":"2020","article_type":"original","date_published":"2020-06-08T00:00:00Z","date_created":"2021-11-26T09:08:19Z","license":"https://creativecommons.org/licenses/by-nc/3.0/","oa":1,"language":[{"iso":"eng"}],"issue":"24","acknowledgement":"We are grateful to the Schiff Foundation (AJD), Peterhouse, Cambridge (TCTM), the Swiss National Science foundation (TCTM), Ramon Jenkins Fellowship, Sidney Sussex, Cambridge (GM), the Royal Society (AŠ), the Academy of Medical Sciences and Wellcome Trust (AŠ), the Danish Research Council (MK), the Lundbeck Foundation (MK), the Swedish Research Council (SL), the Wellcome Trust (TPJK), the Cambridge Centre for Misfolding Diseases (TPJK), the BBSRC (TPJK), the Frances and Augustus Newman Foundation (TPJK) for financial support. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) through the ERC grants PhysProt (agreement no. 337969), MAMBA (agreement no. 340890) and NovoNordiskFonden (SL).","intvolume":"        11","abstract":[{"lang":"eng","text":"The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation."}],"month":"06","volume":11,"external_id":{"pmid":["32953019"]},"pmid":1,"tmp":{"short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png"},"publication_status":"published","author":[{"first_name":"Alexander J.","last_name":"Dear","full_name":"Dear, Alexander J."},{"full_name":"Meisl, Georg","first_name":"Georg","last_name":"Meisl"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Michaels, Thomas C. T.","last_name":"Michaels","first_name":"Thomas C. T."},{"first_name":"Magnus","last_name":"Kjaergaard","full_name":"Kjaergaard, Magnus"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"last_name":"Knowles","first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J."}]},{"language":[{"iso":"eng"}],"acknowledgement":"We acknowledge support from Peterhouse (T.C.T.M.), the Swiss National Science foundation (T.C.T.M.), the Royal Society (A.Š.), the Academy of Medical Sciences (A.Š.), the UCL Institute for the Physics of Living Systems (S.C.), Sidney Sussex College (G.M.), the Wellcome Trust (A.Š., M.V., C.M.D. and T.P.J.K.), the Schiff Foundation (A.J.D.), the Cambridge Centre for Misfolding Diseases (M.V., C.M.D. and T.P.J.K.), the BBSRC (C.M.D. and T.P.J.K.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Swedish Research Council (S.L.) and the ERC grant MAMBA (S.L., agreement no. 340890). The research that led to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969).","oa":1,"issue":"5","intvolume":"        12","date_published":"2020-04-13T00:00:00Z","year":"2020","article_type":"original","date_created":"2021-11-26T09:15:13Z","volume":12,"abstract":[{"text":"Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we found that most Aβ42 oligomers dissociate into their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar structures. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to those of aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.","lang":"eng"}],"month":"04","author":[{"full_name":"Michaels, Thomas C. T.","first_name":"Thomas C. T.","last_name":"Michaels"},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Curk, Samo","first_name":"Samo","last_name":"Curk"},{"last_name":"Bernfur","first_name":"Katja","full_name":"Bernfur, Katja"},{"first_name":"Paolo","last_name":"Arosio","full_name":"Arosio, Paolo"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"last_name":"Dear","first_name":"Alexander J.","full_name":"Dear, Alexander J."},{"full_name":"Cohen, Samuel I. A.","first_name":"Samuel I. A.","last_name":"Cohen"},{"last_name":"Dobson","first_name":"Christopher M.","full_name":"Dobson, Christopher M."},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"full_name":"Linse, Sara","first_name":"Sara","last_name":"Linse"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."}],"external_id":{"pmid":["32303714"]},"publication_status":"published","pmid":1,"publication":"Nature Chemistry","citation":{"ieee":"T. C. T. Michaels <i>et al.</i>, “Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide,” <i>Nature Chemistry</i>, vol. 12, no. 5. Springer Nature, pp. 445–451, 2020.","mla":"Michaels, Thomas C. T., et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>, vol. 12, no. 5, Springer Nature, 2020, pp. 445–51, doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>.","apa":"Michaels, T. C. T., Šarić, A., Curk, S., Bernfur, K., Arosio, P., Meisl, G., … Knowles, T. P. J. (2020). Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>","ama":"Michaels TCT, Šarić A, Curk S, et al. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. <i>Nature Chemistry</i>. 2020;12(5):445-451. doi:<a href=\"https://doi.org/10.1038/s41557-020-0452-1\">10.1038/s41557-020-0452-1</a>","chicago":"Michaels, Thomas C. T., Anđela Šarić, Samo Curk, Katja Bernfur, Paolo Arosio, Georg Meisl, Alexander J. Dear, et al. “Dynamics of Oligomer Populations Formed during the Aggregation of Alzheimer’s Aβ42 Peptide.” <i>Nature Chemistry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41557-020-0452-1\">https://doi.org/10.1038/s41557-020-0452-1</a>.","ista":"Michaels TCT, Šarić A, Curk S, Bernfur K, Arosio P, Meisl G, Dear AJ, Cohen SIA, Dobson CM, Vendruscolo M, Linse S, Knowles TPJ. 2020. Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide. Nature Chemistry. 12(5), 445–451.","short":"T.C.T. Michaels, A. Šarić, S. Curk, K. Bernfur, P. Arosio, G. Meisl, A.J. Dear, S.I.A. Cohen, C.M. Dobson, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Chemistry 12 (2020) 445–451."},"keyword":["general chemical engineering","general chemistry"],"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.01.08.897488"}],"publisher":"Springer Nature","title":"Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide","_id":"10351","date_updated":"2021-11-26T11:21:08Z","day":"13","doi":"10.1038/s41557-020-0452-1","publication_identifier":{"eissn":["1755-4349"],"issn":["1755-4330"]},"quality_controlled":"1","status":"public","scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","page":"445-451","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41557-020-0468-6"}]},"type":"journal_article","extern":"1","article_processing_charge":"No"},{"date_updated":"2025-06-12T06:58:51Z","day":"24","publisher":"Springer Nature","department":[{"_id":"StFr"}],"file":[{"creator":"dernst","file_size":1822469,"content_type":"application/pdf","relation":"main_file","date_created":"2020-09-28T13:16:15Z","access_level":"open_access","file_name":"2020_NatureComm_Prehal.pdf","date_updated":"2020-09-28T13:16:15Z","success":1,"file_id":"8585","checksum":"eada7bc8dd16a49390137cff882ef328"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"citation":{"ista":"Prehal C, Fitzek H, Kothleitner G, Presser V, Gollas B, Freunberger SA, Abbas Q. 2020. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. Nature Communications. 11, 4838.","chicago":"Prehal, Christian, Harald Fitzek, Gerald Kothleitner, Volker Presser, Bernhard Gollas, Stefan Alexander Freunberger, and Qamar Abbas. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>.","short":"C. Prehal, H. Fitzek, G. Kothleitner, V. Presser, B. Gollas, S.A. Freunberger, Q. Abbas, Nature Communications 11 (2020).","apa":"Prehal, C., Fitzek, H., Kothleitner, G., Presser, V., Gollas, B., Freunberger, S. A., &#38; Abbas, Q. (2020). Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18610-6\">https://doi.org/10.1038/s41467-020-18610-6</a>","mla":"Prehal, Christian, et al. “Persistent and Reversible Solid Iodine Electrodeposition in Nanoporous Carbons.” <i>Nature Communications</i>, vol. 11, 4838, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>.","ieee":"C. Prehal <i>et al.</i>, “Persistent and reversible solid iodine electrodeposition in nanoporous carbons,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Prehal C, Fitzek H, Kothleitner G, et al. Persistent and reversible solid iodine electrodeposition in nanoporous carbons. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18610-6\">10.1038/s41467-020-18610-6</a>"},"has_accepted_license":"1","publication":"Nature Communications","_id":"8568","title":"Persistent and reversible solid iodine electrodeposition in nanoporous carbons","ddc":["530"],"article_processing_charge":"No","type":"journal_article","status":"public","quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-020-18610-6","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-020-19720-x"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","volume":11,"month":"09","abstract":[{"lang":"eng","text":"Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries."}],"intvolume":"        11","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","language":[{"iso":"eng"}],"isi":1,"date_created":"2020-09-25T07:23:13Z","article_type":"original","year":"2020","date_published":"2020-09-24T00:00:00Z","file_date_updated":"2020-09-28T13:16:15Z","author":[{"first_name":"Christian","last_name":"Prehal","full_name":"Prehal, Christian"},{"last_name":"Fitzek","first_name":"Harald","full_name":"Fitzek, Harald"},{"last_name":"Kothleitner","first_name":"Gerald","full_name":"Kothleitner, Gerald"},{"first_name":"Volker","last_name":"Presser","full_name":"Presser, Volker"},{"first_name":"Bernhard","last_name":"Gollas","full_name":"Gollas, Bernhard"},{"first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Qamar","last_name":"Abbas","full_name":"Abbas, Qamar"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"4838","pmid":1,"publication_status":"published","corr_author":"1","external_id":{"pmid":["32973214"],"isi":["000573756600004"]}},{"ddc":["570"],"type":"journal_article","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-020-19372-x","status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","date_updated":"2025-06-12T07:01:22Z","day":"04","citation":{"short":"L. Schulte, J. Mao, J. Reitz, S. Sreeramulu, D. Kudlinzki, V.-V. Hodirnau, J. Meier-Credo, K. Saxena, F. Buhr, J.D. Langer, M. Blackledge, A.S. Frangakis, C. Glaubitz, H. Schwalbe, Nature Communications 11 (2020).","chicago":"Schulte, Linda, Jiafei Mao, Julian Reitz, Sridhar Sreeramulu, Denis Kudlinzki, Victor-Valentin Hodirnau, Jakob Meier-Credo, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>.","ista":"Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau V-V, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. 2020. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nature Communications. 11, 5569.","ama":"Schulte L, Mao J, Reitz J, et al. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>","ieee":"L. Schulte <i>et al.</i>, “Cysteine oxidation and disulfide formation in the ribosomal exit tunnel,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Schulte, Linda, et al. “Cysteine Oxidation and Disulfide Formation in the Ribosomal Exit Tunnel.” <i>Nature Communications</i>, vol. 11, 5569, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19372-x\">10.1038/s41467-020-19372-x</a>.","apa":"Schulte, L., Mao, J., Reitz, J., Sreeramulu, S., Kudlinzki, D., Hodirnau, V.-V., … Schwalbe, H. (2020). Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19372-x\">https://doi.org/10.1038/s41467-020-19372-x</a>"},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","publication":"Nature Communications","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"file":[{"date_created":"2020-11-09T07:56:24Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":1670898,"content_type":"application/pdf","success":1,"file_id":"8745","checksum":"b2688f0347e69e6629bba582077278c5","file_name":"2020_NatureComm_Schulte.pdf","date_updated":"2020-11-09T07:56:24Z"}],"title":"Cysteine oxidation and disulfide formation in the ribosomal exit tunnel","_id":"8744","author":[{"first_name":"Linda","last_name":"Schulte","full_name":"Schulte, Linda"},{"first_name":"Jiafei","last_name":"Mao","full_name":"Mao, Jiafei"},{"full_name":"Reitz, Julian","last_name":"Reitz","first_name":"Julian"},{"full_name":"Sreeramulu, Sridhar","last_name":"Sreeramulu","first_name":"Sridhar"},{"last_name":"Kudlinzki","first_name":"Denis","full_name":"Kudlinzki, Denis"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin","orcid":"0000-0003-3904-947X"},{"full_name":"Meier-Credo, Jakob","first_name":"Jakob","last_name":"Meier-Credo"},{"full_name":"Saxena, Krishna","first_name":"Krishna","last_name":"Saxena"},{"full_name":"Buhr, Florian","last_name":"Buhr","first_name":"Florian"},{"full_name":"Langer, Julian D.","last_name":"Langer","first_name":"Julian D."},{"last_name":"Blackledge","first_name":"Martin","full_name":"Blackledge, Martin"},{"first_name":"Achilleas S.","last_name":"Frangakis","full_name":"Frangakis, Achilleas S."},{"full_name":"Glaubitz, Clemens","first_name":"Clemens","last_name":"Glaubitz"},{"last_name":"Schwalbe","first_name":"Harald","full_name":"Schwalbe, Harald"}],"external_id":{"isi":["000592028600001"],"pmid":["33149120"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"article_number":"5569","publication_status":"published","volume":11,"abstract":[{"text":"Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.","lang":"eng"}],"month":"11","language":[{"iso":"eng"}],"acknowledgement":"We acknowledge help from Anja Seybert, Margot Frangakis, Diana Grewe, Mikhail Eltsov, Utz Ermel, and Shintaro Aibara. The work was supported by Deutsche Forschungsgemeinschaft in the CLiC graduate school. Work at the Center for Biomolecular Magnetic Resonance (BMRZ) is supported by the German state of Hesse. The work at BMRZ has been supported by the state of Hesse. L.S. has been supported by the DFG graduate college: CLiC.","oa":1,"isi":1,"intvolume":"        11","article_type":"original","year":"2020","file_date_updated":"2020-11-09T07:56:24Z","date_published":"2020-11-04T00:00:00Z","date_created":"2020-11-09T07:49:36Z"},{"project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367"},{"call_identifier":"FWF","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","_id":"2674F658-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Fäßler","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM"}],"corr_author":"1","external_id":{"isi":["000603078000003"]},"article_number":"6437","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","isi":1,"oa":1,"acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","language":[{"iso":"eng"}],"intvolume":"        11","year":"2020","article_type":"original","file_date_updated":"2020-12-28T08:16:10Z","date_published":"2020-12-22T00:00:00Z","date_created":"2020-12-23T08:25:45Z","volume":11,"abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"month":"12","quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-020-20286-x","status":"public","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage","relation":"press_release"}]},"scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"type":"journal_article","article_processing_charge":"No","citation":{"ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>"},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","publication":"Nature Communications","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"publisher":"Springer Nature","file":[{"relation":"main_file","date_created":"2020-12-28T08:16:10Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":3958727,"success":1,"checksum":"55d43ea0061cc4027ba45e966e1db8cc","file_id":"8975","file_name":"2020_NatureComm_Faessler.pdf","date_updated":"2020-12-28T08:16:10Z"}],"_id":"8971","title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","date_updated":"2025-04-15T07:52:12Z","day":"22"},{"author":[{"full_name":"Youssef, Mena","first_name":"Mena","last_name":"Youssef"},{"full_name":"Morin, Alexandre","first_name":"Alexandre","last_name":"Morin"},{"full_name":"Aubret, Antoine","last_name":"Aubret","first_name":"Antoine"},{"full_name":"Sacanna, Stefano","last_name":"Sacanna","first_name":"Stefano"},{"last_name":"Palacci","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"}],"publication_status":"published","pmid":1,"external_id":{"pmid":["32307507"]},"intvolume":"        16","issue":"17","language":[{"iso":"eng"}],"date_created":"2021-02-01T13:45:11Z","date_published":"2020-05-07T00:00:00Z","year":"2020","article_type":"original","volume":16,"month":"05","abstract":[{"lang":"eng","text":"The fundamental and practical importance of particle stabilization has motivated various characterization methods for studying polymer brushes on particle surfaces. In this work, we show how one can perform sensitive measurements of neutral polymer coating on colloidal particles using a commercial zetameter and salt solutions. By systematically varying the Debye length, we study the mobility of the polymer-coated particles in an applied electric field and show that the electrophoretic mobility of polymer-coated particles normalized by the mobility of non-coated particles is entirely controlled by the polymer brush and independent of the native surface charge, here controlled with pH, or the surface–ion interaction. Our result is rationalized with a simple hydrodynamic model, allowing for the estimation of characteristics of the polymer coating: the brush length L, and the Brinkman length ξ, determined by its resistance to flows. We demonstrate that the Debye layer provides a convenient and faithful probe to the characterization of polymer coatings on particles. Because the method simply relies on a conventional zetameter, it is widely accessible and offers a practical tool to rapidly probe neutral polymer brushes, an asset in the development and utilization of polymer-coated colloidal particles."}],"status":"public","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"doi":"10.1039/c9sm01850f","quality_controlled":"1","scopus_import":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"None","page":"4274-4282","article_processing_charge":"No","extern":"1","type":"journal_article","publisher":"Royal Society of Chemistry ","publication":"Soft Matter","citation":{"ieee":"M. Youssef, A. Morin, A. Aubret, S. Sacanna, and J. A. Palacci, “Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt,” <i>Soft Matter</i>, vol. 16, no. 17. Royal Society of Chemistry , pp. 4274–4282, 2020.","apa":"Youssef, M., Morin, A., Aubret, A., Sacanna, S., &#38; Palacci, J. A. (2020). Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>","mla":"Youssef, Mena, et al. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” <i>Soft Matter</i>, vol. 16, no. 17, Royal Society of Chemistry , 2020, pp. 4274–82, doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>.","ama":"Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. <i>Soft Matter</i>. 2020;16(17):4274-4282. doi:<a href=\"https://doi.org/10.1039/c9sm01850f\">10.1039/c9sm01850f</a>","chicago":"Youssef, Mena, Alexandre Morin, Antoine Aubret, Stefano Sacanna, and Jérémie A Palacci. “Rapid Characterization of Neutral Polymer Brush with a Conventional Zetameter and a Variable Pinch of Salt.” <i>Soft Matter</i>. Royal Society of Chemistry , 2020. <a href=\"https://doi.org/10.1039/c9sm01850f\">https://doi.org/10.1039/c9sm01850f</a>.","ista":"Youssef M, Morin A, Aubret A, Sacanna S, Palacci JA. 2020. Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt. Soft Matter. 16(17), 4274–4282.","short":"M. Youssef, A. Morin, A. Aubret, S. Sacanna, J.A. Palacci, Soft Matter 16 (2020) 4274–4282."},"keyword":["General Chemistry","Condensed Matter Physics"],"_id":"9054","title":"Rapid characterization of neutral polymer brush with a conventional zetameter and a variable pinch of salt","date_updated":"2023-02-23T13:47:45Z","day":"07"},{"publication_identifier":{"issn":["2046-2069"]},"doi":"10.1039/d0ra05394e","quality_controlled":"1","status":"public","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","oa_version":"Published Version","page":"28383-28389","extern":"1","type":"journal_article","article_processing_charge":"No","publication":"RSC Advances","keyword":["General Chemistry","General Chemical Engineering"],"citation":{"ama":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. 2020;10(47):28383-28389. doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>","apa":"Nauman, M., Alnasir, M. H., Hamayun, M. A., Wang, Y., Shatruk, M., &#38; Manzoor, S. (2020). Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. <i>RSC Advances</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>","mla":"Nauman, Muhammad, et al. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>, vol. 10, no. 47, Royal Society of Chemistry, 2020, pp. 28383–89, doi:<a href=\"https://doi.org/10.1039/d0ra05394e\">10.1039/d0ra05394e</a>.","ieee":"M. Nauman, M. H. Alnasir, M. A. Hamayun, Y. Wang, M. Shatruk, and S. Manzoor, “Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles,” <i>RSC Advances</i>, vol. 10, no. 47. Royal Society of Chemistry, pp. 28383–28389, 2020.","short":"M. Nauman, M.H. Alnasir, M.A. Hamayun, Y. Wang, M. Shatruk, S. Manzoor, RSC Advances 10 (2020) 28383–28389.","ista":"Nauman M, Alnasir MH, Hamayun MA, Wang Y, Shatruk M, Manzoor S. 2020. Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles. RSC Advances. 10(47), 28383–28389.","chicago":"Nauman, Muhammad, Muhammad Hisham Alnasir, Muhammad Asif Hamayun, YiXu Wang, Michael Shatruk, and Sadia Manzoor. “Size-Dependent Magnetic and Magnetothermal Properties of Gadolinium Silicide Nanoparticles.” <i>RSC Advances</i>. Royal Society of Chemistry, 2020. <a href=\"https://doi.org/10.1039/d0ra05394e\">https://doi.org/10.1039/d0ra05394e</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/d0ra05394e"}],"publisher":"Royal Society of Chemistry","OA_place":"publisher","_id":"9067","title":"Size-dependent magnetic and magnetothermal properties of gadolinium silicide nanoparticles","date_updated":"2024-10-15T13:44:01Z","OA_type":"gold","day":"29","DOAJ_listed":"1","author":[{"last_name":"Nauman","first_name":"Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","full_name":"Nauman, Muhammad","orcid":"0000-0002-2111-4846"},{"full_name":"Alnasir, Muhammad Hisham","last_name":"Alnasir","first_name":"Muhammad Hisham"},{"full_name":"Hamayun, Muhammad Asif","last_name":"Hamayun","first_name":"Muhammad Asif"},{"first_name":"YiXu","last_name":"Wang","full_name":"Wang, YiXu"},{"first_name":"Michael","last_name":"Shatruk","full_name":"Shatruk, Michael"},{"last_name":"Manzoor","first_name":"Sadia","full_name":"Manzoor, Sadia"}],"publication_status":"published","language":[{"iso":"eng"}],"oa":1,"issue":"47","intvolume":"        10","date_published":"2020-07-29T00:00:00Z","article_type":"original","year":"2020","date_created":"2021-02-02T15:51:23Z","volume":10,"abstract":[{"text":"Gadolinium silicide (Gd5Si4) nanoparticles are an interesting class of materials due to their high magnetization, low Curie temperature, low toxicity in biological environments and their multifunctional properties. We report the magnetic and magnetothermal properties of gadolinium silicide (Gd5Si4) nanoparticles prepared by surfactant-assisted ball milling of arc melted bulk ingots of the compound. Using different milling times and speeds, a wide range of crystallite sizes (13–43 nm) could be produced and a reduction in Curie temperature (TC) from 340 K to 317 K was achieved, making these nanoparticles suitable for self-controlled magnetic hyperthermia applications. The magnetothermal effect was measured in applied AC magnetic fields of amplitude 164–239 Oe and frequencies 163–519 kHz. All particles showed magnetic heating with a strong dependence of the specific absorption rate (SAR) on the average crystallite size. The highest SAR of 3.7 W g−1 was measured for 43 nm sized nanoparticles of Gd5Si4. The high SAR and low TC, (within the therapeutic range for magnetothermal therapy) makes the Gd5Si4 behave like self-regulating heat switches that would be suitable for self-controlled magnetic hyperthermia applications after biocompatibility and cytotoxicity tests.","lang":"eng"}],"month":"07"},{"author":[{"last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876"},{"first_name":"Matthias","last_name":"Wulf","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena","last_name":"Redchenko"},{"orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","last_name":"Hassani","first_name":"Farid"},{"last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"4460","pmid":1,"publication_status":"published","corr_author":"1","external_id":{"pmid":["32901014"],"isi":["000577280200001"]},"project":[{"grant_number":"732894","call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"grant_number":"758053","call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Quantum readout techniques and technologies","grant_number":"862644","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"}],"volume":11,"acknowledged_ssus":[{"_id":"NanoFab"}],"month":"09","abstract":[{"lang":"eng","text":"Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a <jats:italic>V</jats:italic><jats:sub><jats:italic>π</jats:italic></jats:sub> as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform."}],"intvolume":"        11","oa":1,"acknowledgement":"We thank Yuan Chen for performing supplementary FEM simulations and Andrew Higginbotham, Ralf Riedinger, Sungkun Hong, and Lorenzo Magrini for valuable discussions. This work was supported by IST Austria, the IST nanofabrication facility (NFF), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 732894 (FET Proactive HOT) and the European Research Council under grant agreement no. 758053 (ERC StG QUNNECT). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 754411. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and innovation program under grant agreement no. 862644 (FET Open QUARTET).","language":[{"iso":"eng"}],"isi":1,"date_created":"2020-09-18T10:56:20Z","article_type":"original","year":"2020","file_date_updated":"2020-09-18T13:02:37Z","date_published":"2020-09-08T00:00:00Z","ddc":["530"],"article_processing_charge":"No","type":"journal_article","status":"public","ec_funded":1,"quality_controlled":"1","publication_identifier":{"issn":["2041-1723"]},"doi":"10.1038/s41467-020-18269-z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41467-020-18912-9","relation":"erratum"},{"url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"13056","relation":"research_data","status":"public"},{"status":"public","id":"18871","relation":"dissertation_contains"}]},"oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-28T22:30:25Z","day":"08","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"file":[{"content_type":"application/pdf","file_size":1002818,"creator":"dernst","access_level":"open_access","date_created":"2020-09-18T13:02:37Z","relation":"main_file","date_updated":"2020-09-18T13:02:37Z","file_name":"2020_NatureComm_Arnold.pdf","checksum":"88f92544889eb18bb38e25629a422a86","file_id":"8530","success":1}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"citation":{"mla":"Arnold, Georg M., et al. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>, vol. 11, 4460, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>","ieee":"G. M. Arnold <i>et al.</i>, “Converting microwave and telecom photons with a silicon photonic nanomechanical interface,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-18269-z\">10.1038/s41467-020-18269-z</a>","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Nature Communications. 11, 4460.","chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-18269-z\">https://doi.org/10.1038/s41467-020-18269-z</a>.","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, Nature Communications 11 (2020)."},"publication":"Nature Communications","has_accepted_license":"1","_id":"8529","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface"},{"type":"journal_article","extern":"1","article_processing_charge":"No","quality_controlled":"1","doi":"10.1021/acs.nanolett.9b02642","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"status":"public","page":"7106-7111","oa_version":"None","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-14T12:13:57Z","day":"20","keyword":["Mechanical Engineering","Condensed Matter Physics","General Materials Science","General Chemistry","Bioengineering"],"citation":{"ista":"Chu Z, Klajn R. 2019. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. Nano Letters. 19(10), 7106–7111.","chicago":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” <i>Nano Letters</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.nanolett.9b02642\">https://doi.org/10.1021/acs.nanolett.9b02642</a>.","short":"Z. Chu, R. Klajn, Nano Letters 19 (2019) 7106–7111.","mla":"Chu, Zonglin, and Rafal Klajn. “Polysilsesquioxane Nanowire Networks as an ‘Artificial Solvent’ for Reversible Operation of Photochromic Molecules.” <i>Nano Letters</i>, vol. 19, no. 10, American Chemical Society, 2019, pp. 7106–11, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b02642\">10.1021/acs.nanolett.9b02642</a>.","apa":"Chu, Z., &#38; Klajn, R. (2019). Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.9b02642\">https://doi.org/10.1021/acs.nanolett.9b02642</a>","ieee":"Z. Chu and R. Klajn, “Polysilsesquioxane nanowire networks as an ‘Artificial Solvent’ for reversible operation of photochromic molecules,” <i>Nano Letters</i>, vol. 19, no. 10. American Chemical Society, pp. 7106–7111, 2019.","ama":"Chu Z, Klajn R. Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules. <i>Nano Letters</i>. 2019;19(10):7106-7111. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.9b02642\">10.1021/acs.nanolett.9b02642</a>"},"publication":"Nano Letters","publisher":"American Chemical Society","_id":"13370","title":"Polysilsesquioxane nanowire networks as an “Artificial Solvent” for reversible operation of photochromic molecules","author":[{"full_name":"Chu, Zonglin","first_name":"Zonglin","last_name":"Chu"},{"last_name":"Klajn","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal"}],"external_id":{"pmid":["31539469"]},"pmid":1,"publication_status":"published","volume":19,"abstract":[{"lang":"eng","text":"Efficient isomerization of photochromic molecules often requires conformational freedom and is typically not available under solvent-free conditions. Here, we report a general methodology allowing for reversible switching of such molecules on the surfaces of solid materials. Our method is based on dispersing photochromic compounds within polysilsesquioxane nanowire networks (PNNs), which can be fabricated as transparent, highly porous, micrometer-thick layers on various substrates. We found that azobenzene switching within the PNNs proceeded unusually fast compared with the same molecules in liquid solvents. Efficient isomerization of another photochromic system, spiropyran, from a colorless to a colored form was used to create reversible images in PNN-coated glass. The coloration reaction could be induced with sunlight and is of interest for developing “smart” windows."}],"month":"09","issue":"10","language":[{"iso":"eng"}],"intvolume":"        19","article_type":"original","year":"2019","date_published":"2019-09-20T00:00:00Z","date_created":"2023-08-01T09:38:23Z"},{"issue":"9","oa":1,"language":[{"iso":"eng"}],"intvolume":"         5","date_published":"2019-09-12T00:00:00Z","article_type":"original","year":"2019","date_created":"2023-08-01T09:38:38Z","volume":5,"abstract":[{"lang":"eng","text":"Diamondoid nanoporous crystals represent a synthetically challenging class of materials that typically have been obtained from tetrahedral building blocks. In this issue of Chem, Stoddart and coworkers demonstrate that it is possible to generate diamondoid frameworks from a hexacationic building block lacking a tetrahedral symmetry. These results highlight the great potential of self-assembly for rapidly transforming small molecules into structurally complex functional materials."}],"month":"09","author":[{"last_name":"Białek","first_name":"Michał J.","full_name":"Białek, Michał J."},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"publication_status":"published","publication":"Chem","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"citation":{"ama":"Białek MJ, Klajn R. Diamond grows up. <i>Chem</i>. 2019;5(9):2283-2285. doi:<a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">10.1016/j.chempr.2019.08.012</a>","apa":"Białek, M. J., &#38; Klajn, R. (2019). Diamond grows up. <i>Chem</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">https://doi.org/10.1016/j.chempr.2019.08.012</a>","mla":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” <i>Chem</i>, vol. 5, no. 9, Elsevier, 2019, pp. 2283–85, doi:<a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">10.1016/j.chempr.2019.08.012</a>.","ieee":"M. J. Białek and R. Klajn, “Diamond grows up,” <i>Chem</i>, vol. 5, no. 9. Elsevier, pp. 2283–2285, 2019.","short":"M.J. Białek, R. Klajn, Chem 5 (2019) 2283–2285.","ista":"Białek MJ, Klajn R. 2019. Diamond grows up. Chem. 5(9), 2283–2285.","chicago":"Białek, Michał J., and Rafal Klajn. “Diamond Grows Up.” <i>Chem</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chempr.2019.08.012\">https://doi.org/10.1016/j.chempr.2019.08.012</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2019.08.012"}],"publisher":"Elsevier","title":"Diamond grows up","_id":"13371","date_updated":"2024-10-14T12:14:05Z","day":"12","publication_identifier":{"eissn":["2451-9294"],"issn":["2451-9308"]},"doi":"10.1016/j.chempr.2019.08.012","quality_controlled":"1","status":"public","oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2283-2285","type":"journal_article","extern":"1","article_processing_charge":"No"},{"citation":{"ama":"Grzelczak M, Liz-Marzán LM, Klajn R. Stimuli-responsive self-assembly of nanoparticles. <i>Chemical Society Reviews</i>. 2019;48(5):1342-1361. doi:<a href=\"https://doi.org/10.1039/c8cs00787j\">10.1039/c8cs00787j</a>","ieee":"M. Grzelczak, L. M. Liz-Marzán, and R. Klajn, “Stimuli-responsive self-assembly of nanoparticles,” <i>Chemical Society Reviews</i>, vol. 48, no. 5. Royal Society of Chemistry, pp. 1342–1361, 2019.","mla":"Grzelczak, Marek, et al. “Stimuli-Responsive Self-Assembly of Nanoparticles.” <i>Chemical Society Reviews</i>, vol. 48, no. 5, Royal Society of Chemistry, 2019, pp. 1342–61, doi:<a href=\"https://doi.org/10.1039/c8cs00787j\">10.1039/c8cs00787j</a>.","apa":"Grzelczak, M., Liz-Marzán, L. M., &#38; Klajn, R. (2019). Stimuli-responsive self-assembly of nanoparticles. <i>Chemical Society Reviews</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8cs00787j\">https://doi.org/10.1039/c8cs00787j</a>","short":"M. Grzelczak, L.M. Liz-Marzán, R. Klajn, Chemical Society Reviews 48 (2019) 1342–1361.","chicago":"Grzelczak, Marek, Luis M. Liz-Marzán, and Rafal Klajn. “Stimuli-Responsive Self-Assembly of Nanoparticles.” <i>Chemical Society Reviews</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c8cs00787j\">https://doi.org/10.1039/c8cs00787j</a>.","ista":"Grzelczak M, Liz-Marzán LM, Klajn R. 2019. Stimuli-responsive self-assembly of nanoparticles. Chemical Society Reviews. 48(5), 1342–1361."},"keyword":["General Chemistry"],"publication":"Chemical Society Reviews","publisher":"Royal Society of Chemistry","main_file_link":[{"url":"https://doi.org/10.1039/C8CS00787J","open_access":"1"}],"title":"Stimuli-responsive self-assembly of nanoparticles","_id":"13372","date_updated":"2024-10-14T12:14:14Z","day":"28","quality_controlled":"1","doi":"10.1039/c8cs00787j","publication_identifier":{"eissn":["1460-4744"],"issn":["0306-0012"]},"status":"public","page":"1342-1361","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","extern":"1","type":"journal_article","article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}],"issue":"5","intvolume":"        48","article_type":"original","year":"2019","date_published":"2019-01-28T00:00:00Z","date_created":"2023-08-01T09:38:52Z","volume":48,"abstract":[{"text":"The capacity to respond or adapt to environmental changes is an intrinsic property of living systems that comprise highly-connected subcomponents communicating through chemical networks. The development of responsive synthetic systems is a relatively new research area that covers different disciplines, among which nanochemistry brings conceptually new demonstrations. Especially attractive are ligand-protected gold nanoparticles, which have been extensively used over the last decade as building blocks in constructing superlattices or dynamic aggregates, under the effect of an applied stimulus. To reflect the importance of surface chemistry and nanoparticle core composition in the dynamic self-assembly of nanoparticles, we provide here an overview of various available stimuli, as tools for synthetic chemists to exploit. Along with this task, the review starts with the use of chemical stimuli such as solvent, pH, gases, metal ions or biomolecules. It then focuses on physical stimuli: temperature, magnetic and electric fields, as well as light. To reflect on the increasing complexity of current architectures, we discuss systems that are responsive to more than one stimulus, to finally encourage further research by proposing future challenges.","lang":"eng"}],"month":"01","author":[{"first_name":"Marek","last_name":"Grzelczak","full_name":"Grzelczak, Marek"},{"first_name":"Luis M.","last_name":"Liz-Marzán","full_name":"Liz-Marzán, Luis M."},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","full_name":"Klajn, Rafal","last_name":"Klajn","first_name":"Rafal"}],"external_id":{"pmid":["30688963"]},"pmid":1,"publication_status":"published"},{"external_id":{"pmid":["30595017"]},"pmid":1,"publication_status":"published","author":[{"full_name":"Chu, Zonglin","first_name":"Zonglin","last_name":"Chu"},{"full_name":"Han, Yanxiao","last_name":"Han","first_name":"Yanxiao"},{"last_name":"Bian","first_name":"Tong","full_name":"Bian, Tong"},{"full_name":"De, Soumen","first_name":"Soumen","last_name":"De"},{"last_name":"Král","first_name":"Petr","full_name":"Král, Petr"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"year":"2019","article_type":"original","date_published":"2019-02-06T00:00:00Z","date_created":"2023-08-01T09:39:19Z","language":[{"iso":"eng"}],"issue":"5","intvolume":"       141","abstract":[{"text":"The reversible photoisomerization of azobenzene has been utilized to construct a plethora of systems in which optical, electronic, catalytic, and other properties can be controlled by light. However, owing to azobenzene’s hydrophobic nature, most of these examples have been realized only in organic solvents, and systems operating in water are relatively scarce. Here, we show that by coadsorbing the inherently hydrophobic azobenzenes with water-solubilizing ligands on the same nanoparticulate platforms, it is possible to render them essentially water-soluble. To this end, we developed a modified nanoparticle functionalization procedure allowing us to precisely fine-tune the amount of azobenzene on the functionalized nanoparticles. Molecular dynamics simulations helped us to identify two distinct supramolecular architectures (depending on the length of the background ligand) on these nanoparticles, which can explain their excellent aqueous solubilities. Azobenzenes adsorbed on these water-soluble nanoparticles exhibit highly reversible photoisomerization upon exposure to UV and visible light. Importantly, the mixed-monolayer approach allowed us to systematically investigate how the background ligand affects the switching properties of azobenzene. We found that the nature of the background ligand has a profound effect on the kinetics of azobenzene switching. For example, a hydroxy-terminated background ligand is capable of accelerating the back-isomerization reaction by more than 6000-fold. These results pave the way toward the development of novel light-responsive nanomaterials operating in aqueous media and, in the long run, in biological environments.","lang":"eng"}],"month":"02","volume":141,"page":"1949-1960","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"doi":"10.1021/jacs.8b09638","status":"public","type":"journal_article","extern":"1","article_processing_charge":"No","title":"Supramolecular control of azobenzene switching on nanoparticles","_id":"13373","citation":{"chicago":"Chu, Zonglin, Yanxiao Han, Tong Bian, Soumen De, Petr Král, and Rafal Klajn. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.8b09638\">https://doi.org/10.1021/jacs.8b09638</a>.","ista":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. 2019. Supramolecular control of azobenzene switching on nanoparticles. Journal of the American Chemical Society. 141(5), 1949–1960.","short":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, R. Klajn, Journal of the American Chemical Society 141 (2019) 1949–1960.","ieee":"Z. Chu, Y. Han, T. Bian, S. De, P. Král, and R. Klajn, “Supramolecular control of azobenzene switching on nanoparticles,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 5. American Chemical Society, pp. 1949–1960, 2019.","apa":"Chu, Z., Han, Y., Bian, T., De, S., Král, P., &#38; Klajn, R. (2019). Supramolecular control of azobenzene switching on nanoparticles. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.8b09638\">https://doi.org/10.1021/jacs.8b09638</a>","mla":"Chu, Zonglin, et al. “Supramolecular Control of Azobenzene Switching on Nanoparticles.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 5, American Chemical Society, 2019, pp. 1949–60, doi:<a href=\"https://doi.org/10.1021/jacs.8b09638\">10.1021/jacs.8b09638</a>.","ama":"Chu Z, Han Y, Bian T, De S, Král P, Klajn R. Supramolecular control of azobenzene switching on nanoparticles. <i>Journal of the American Chemical Society</i>. 2019;141(5):1949-1960. doi:<a href=\"https://doi.org/10.1021/jacs.8b09638\">10.1021/jacs.8b09638</a>"},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","day":"06","date_updated":"2024-10-14T12:14:23Z"}]