[{"year":"2018","publication":"Nano Letters","day":"18","page":"5350-5356","date_created":"2021-11-26T12:15:47Z","date_published":"2018-04-18T00:00:00Z","doi":"10.1021/acs.nanolett.8b00786","acknowledgement":"We acknowledge discussions with Giuseppe Battaglia as well as support from the Herchel Smith scholarship (T.C.), the CAS PIFI fellowship (T.C.), the UCL Institute for the Physics of Living Systems (T.C. and A.Š.), the Austrian Academy of Sciences through a DOC fellowship (P.W.), the European Union Horizon 2020 programme under ETN grant no. 674979-NANOTRANS and FET grant no. 766972-NANOPHLOW (J.D. and D.F.), the Engineering and Physical Sciences Research Council (D.F. and A.Š.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (A.Š.). We thank Claudia Flandoli for help with Figure 1.","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","citation":{"chicago":"Curk, Tine, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, and Anđela Šarić. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b00786.","ista":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. 2018. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 18(9), 5350–5356.","mla":"Curk, Tine, et al. “Controlling Cargo Trafficking in Multicomponent Membranes.” Nano Letters, vol. 18, no. 9, American Chemical Society, 2018, pp. 5350–56, doi:10.1021/acs.nanolett.8b00786.","apa":"Curk, T., Wirnsberger, P., Dobnikar, J., Frenkel, D., & Šarić, A. (2018). Controlling cargo trafficking in multicomponent membranes. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b00786","ama":"Curk T, Wirnsberger P, Dobnikar J, Frenkel D, Šarić A. Controlling cargo trafficking in multicomponent membranes. Nano Letters. 2018;18(9):5350-5356. doi:10.1021/acs.nanolett.8b00786","ieee":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, and A. Šarić, “Controlling cargo trafficking in multicomponent membranes,” Nano Letters, vol. 18, no. 9. American Chemical Society, pp. 5350–5356, 2018.","short":"T. Curk, P. Wirnsberger, J. Dobnikar, D. Frenkel, A. Šarić, Nano Letters 18 (2018) 5350–5356."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["29667410"]},"author":[{"last_name":"Curk","full_name":"Curk, Tine","first_name":"Tine"},{"first_name":"Peter","last_name":"Wirnsberger","full_name":"Wirnsberger, Peter"},{"first_name":"Jure","full_name":"Dobnikar, Jure","last_name":"Dobnikar"},{"first_name":"Daan","full_name":"Frenkel, Daan","last_name":"Frenkel"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"}],"title":"Controlling cargo trafficking in multicomponent membranes","publication_status":"published","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"language":[{"iso":"eng"}],"issue":"9","volume":18,"abstract":[{"lang":"eng","text":"Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such “inert” components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets."}],"pmid":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1712.10147","open_access":"1"}],"scopus_import":"1","intvolume":" 18","month":"04","date_updated":"2021-11-26T15:14:08Z","extern":"1","_id":"10359","type":"journal_article","article_type":"original","keyword":["mechanical engineering","condensed matter physics"],"status":"public"},{"publication_status":"published","publication_identifier":{"issn":["0026-8976"],"eissn":["1362-3028"]},"language":[{"iso":"eng"}],"issue":"21-22","volume":116,"abstract":[{"text":"Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1803.04851","open_access":"1"}],"scopus_import":"1","intvolume":" 116","month":"05","date_updated":"2021-11-26T12:39:58Z","extern":"1","_id":"10358","article_type":"original","type":"journal_article","keyword":["physical chemistry"],"status":"public","year":"2018","publication":"Molecular Physics","day":"24","page":"3055-3065","date_created":"2021-11-26T12:08:02Z","date_published":"2018-05-24T00:00:00Z","doi":"10.1080/00268976.2018.1474280","acknowledgement":"We thank Claudia Flandoli for the help with illustrations.","oa":1,"quality_controlled":"1","publisher":"Taylor & Francis","citation":{"chicago":"Michaels, Thomas C. T., Lucie X. Liu, Samo Curk, Peter G. Bolhuis, Anđela Šarić, and Tuomas P. J. Knowles. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics. Taylor & Francis, 2018. https://doi.org/10.1080/00268976.2018.1474280.","ista":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. 2018. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 116(21–22), 3055–3065.","mla":"Michaels, Thomas C. T., et al. “Reaction Rate Theory for Supramolecular Kinetics: Application to Protein Aggregation.” Molecular Physics, vol. 116, no. 21–22, Taylor & Francis, 2018, pp. 3055–65, doi:10.1080/00268976.2018.1474280.","ieee":"T. C. T. Michaels, L. X. Liu, S. Curk, P. G. Bolhuis, A. Šarić, and T. P. J. Knowles, “Reaction rate theory for supramolecular kinetics: application to protein aggregation,” Molecular Physics, vol. 116, no. 21–22. Taylor & Francis, pp. 3055–3065, 2018.","short":"T.C.T. Michaels, L.X. Liu, S. Curk, P.G. Bolhuis, A. Šarić, T.P.J. Knowles, Molecular Physics 116 (2018) 3055–3065.","apa":"Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2018.1474280","ama":"Michaels TCT, Liu LX, Curk S, Bolhuis PG, Šarić A, Knowles TPJ. Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics. 2018;116(21-22):3055-3065. doi:10.1080/00268976.2018.1474280"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"arxiv":["1803.04851"]},"author":[{"first_name":"Thomas C. T.","last_name":"Michaels","full_name":"Michaels, Thomas C. T."},{"full_name":"Liu, Lucie X.","last_name":"Liu","first_name":"Lucie X."},{"first_name":"Samo","full_name":"Curk, Samo","last_name":"Curk"},{"full_name":"Bolhuis, Peter G.","last_name":"Bolhuis","first_name":"Peter G."},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"}],"title":"Reaction rate theory for supramolecular kinetics: application to protein aggregation"},{"acknowledgement":"We acknowledge support from the Swiss National Science Foundation (T.C.T.M.); Peterhouse,\r\nCambridge (T.C.T.M.); the Royal Society (A.S.); the Academy of Medical Sciences (A.S.); the\r\nWellcome Trust (A.S., M.V., C.M.D., T.P.J.K.); the Cambridge Centre for Misfolding Diseases\r\n(M.V., C.M.D., T.P.J.K.); the Biotechnology and Biological Sciences Research Council (C.M.D.,\r\nT.P.J.K.); and the Frances and Augustus Newman Foundation (T.P.J.K.). The research leading\r\nto these results has received funding from the European Research Council (ERC) under the\r\nEuropean Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant\r\nPhysProt (337969).","quality_controlled":"1","publisher":"Annual Reviews","year":"2018","publication":"Annual Review of Physical Chemistry","day":"28","page":"273-298","date_created":"2021-11-26T12:52:12Z","doi":"10.1146/annurev-physchem-050317-021322","date_published":"2018-02-28T00:00:00Z","citation":{"chicago":"Michaels, Thomas C.T., Anđela Šarić, Johnny Habchi, Sean Chia, Georg Meisl, Michele Vendruscolo, Christopher M. Dobson, and Tuomas P.J. Knowles. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry. Annual Reviews, 2018. https://doi.org/10.1146/annurev-physchem-050317-021322.","ista":"Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. 2018. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 69(1), 273–298.","mla":"Michaels, Thomas C. T., et al. “Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.” Annual Review of Physical Chemistry, vol. 69, no. 1, Annual Reviews, 2018, pp. 273–98, doi:10.1146/annurev-physchem-050317-021322.","short":"T.C.T. Michaels, A. Šarić, J. Habchi, S. Chia, G. Meisl, M. Vendruscolo, C.M. Dobson, T.P.J. Knowles, Annual Review of Physical Chemistry 69 (2018) 273–298.","ieee":"T. C. T. Michaels et al., “Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation,” Annual Review of Physical Chemistry, vol. 69, no. 1. Annual Reviews, pp. 273–298, 2018.","apa":"Michaels, T. C. T., Šarić, A., Habchi, J., Chia, S., Meisl, G., Vendruscolo, M., … Knowles, T. P. J. (2018). Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. Annual Reviews. https://doi.org/10.1146/annurev-physchem-050317-021322","ama":"Michaels TCT, Šarić A, Habchi J, et al. Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation. Annual Review of Physical Chemistry. 2018;69(1):273-298. doi:10.1146/annurev-physchem-050317-021322"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","external_id":{"pmid":["29490200"]},"author":[{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"last_name":"Habchi","full_name":"Habchi, Johnny","first_name":"Johnny"},{"first_name":"Sean","full_name":"Chia, Sean","last_name":"Chia"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"full_name":"Dobson, Christopher M.","last_name":"Dobson","first_name":"Christopher M."},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}],"title":"Chemical kinetics for bridging molecular mechanisms and macroscopic measurements of amyloid fibril formation","abstract":[{"text":"Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","intvolume":" 69","month":"02","publication_status":"published","publication_identifier":{"eissn":["1545-1593"],"issn":["0066-426X"]},"language":[{"iso":"eng"}],"issue":"1","volume":69,"_id":"10361","article_type":"original","type":"journal_article","keyword":["physical and theoretical chemistry"],"status":"public","date_updated":"2021-11-26T15:58:19Z","extern":"1"},{"article_number":"226801","citation":{"short":"H. Polshyn, H. Zhou, E.M. Spanton, T. Taniguchi, K. Watanabe, A.F. Young, Physical Review Letters 121 (2018).","ieee":"H. Polshyn, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young, “Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices,” Physical Review Letters, vol. 121, no. 22. American Physical Society, 2018.","apa":"Polshyn, H., Zhou, H., Spanton, E. M., Taniguchi, T., Watanabe, K., & Young, A. F. (2018). Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.226801","ama":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 2018;121(22). doi:10.1103/physrevlett.121.226801","mla":"Polshyn, Hryhoriy, et al. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters, vol. 121, no. 22, 226801, American Physical Society, 2018, doi:10.1103/physrevlett.121.226801.","ista":"Polshyn H, Zhou H, Spanton EM, Taniguchi T, Watanabe K, Young AF. 2018. Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices. Physical Review Letters. 121(22), 226801.","chicago":"Polshyn, Hryhoriy, H. Zhou, E. M. Spanton, T. Taniguchi, K. Watanabe, and A. F. Young. “Quantitative Transport Measurements of Fractional Quantum Hall Energy Gaps in Edgeless Graphene Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.226801."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Polshyn","orcid":"0000-0001-8223-8896","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48"},{"first_name":"H.","last_name":"Zhou","full_name":"Zhou, H."},{"first_name":"E. M.","last_name":"Spanton","full_name":"Spanton, E. M."},{"first_name":"T.","last_name":"Taniguchi","full_name":"Taniguchi, T."},{"first_name":"K.","full_name":"Watanabe, K.","last_name":"Watanabe"},{"full_name":"Young, A. F.","last_name":"Young","first_name":"A. F."}],"external_id":{"arxiv":["1805.04199"]},"article_processing_charge":"No","title":"Quantitative transport measurements of fractional quantum Hall energy gaps in edgeless graphene devices","acknowledgement":"We thank Cory Dean, S. Chen, Y. Zeng, M. Yankowitz, and J. Li for discussing their unpublished data and for sharing the stack inversion technique. The authors acknowledge further discussions of the results with I. Sodemann, M. Zaletel, C. Nayak, and J. Jain. A. F. Y., H. P., H. Z., and E. M. S. were supported by the ARO under awards 69188PHH and MURI W911NF-17-1-0323. A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the MEXT, Japan, and JSPS KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Prize Fellowship in Science of the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard Foundation.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"year":"2018","day":"28","publication":"Physical Review Letters","doi":"10.1103/physrevlett.121.226801","date_published":"2018-11-28T00:00:00Z","date_created":"2022-01-14T12:15:47Z","_id":"10626","article_type":"original","type":"journal_article","status":"public","keyword":["general physics and astronomy"],"date_updated":"2022-01-14T13:48:35Z","extern":"1","abstract":[{"text":"Owing to their wide tunability, multiple internal degrees of freedom, and low disorder, graphene heterostructures are emerging as a promising experimental platform for fractional quantum Hall (FQH) studies. Here, we report FQH thermal activation gap measurements in dual graphite-gated monolayer graphene devices fabricated in an edgeless Corbino geometry. In devices with substrate-induced sublattice splitting, we find a tunable crossover between single- and multicomponent FQH states in the zero energy Landau level. Activation gaps in the single-component regime show excellent agreement with numerical calculations using a single broadening parameter \r\nΓ≈7.2K. In the first excited Landau level, in contrast, FQH gaps are strongly influenced by Landau level mixing, and we observe an unexpected valley-ordered state at integer filling ν=−4.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.04199"}],"month":"11","intvolume":" 121","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":121,"issue":"22"},{"issue":"18","volume":97,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"intvolume":" 97","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1703.08184","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present a scanning probe technique for measuring the dynamics of individual fluxoid transitions in multiply connected superconducting structures. In these measurements, a small magnetic particle attached to the tip of a silicon cantilever is scanned over a micron-size superconducting ring fabricated from a thin aluminum film. We find that near the superconducting transition temperature of the aluminum, the dissipation and frequency of the cantilever changes significantly at particular locations where the tip-induced magnetic flux penetrating the ring causes the two lowest-energy fluxoid states to become nearly degenerate. In this regime, we show that changes in the cantilever frequency and dissipation are well-described by a stochastic resonance (SR) process, wherein small oscillations of the cantilever in the presence of thermally activated phase slips (TAPS) in the ring give rise to a dynamical force that modifies the mechanical properties of the cantilever. Using the SR model, we calculate the average fluctuation rate of the TAPS as a function of temperature over a 32-dB range in frequency, and we compare it to the Langer-Ambegaokar-McCumber-Halperin theory for TAPS in one-dimensional superconducting structures."}],"extern":"1","date_updated":"2022-01-14T13:58:24Z","status":"public","type":"journal_article","article_type":"original","_id":"10627","date_created":"2022-01-14T13:48:47Z","doi":"10.1103/physrevb.97.184501","date_published":"2018-05-08T00:00:00Z","publication":"Physical Review B","day":"08","year":"2018","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We are grateful to Nadya Mason for useful discussions. This work was supported by the DOE Basic Energy Sciences under Contract No. DE-SC0012649, the Department of Physics and the Frederick Seitz Materials Research Laboratory Central Facilities at the University of Illinois.\r\n","title":"Imaging phase slip dynamics in micron-size superconducting rings","external_id":{"arxiv":["1703.08184"]},"article_processing_charge":"No","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","first_name":"Hryhoriy","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","orcid":"0000-0001-8223-8896"},{"first_name":"Tyler R.","full_name":"Naibert, Tyler R.","last_name":"Naibert"},{"first_name":"Raffi","last_name":"Budakian","full_name":"Budakian, Raffi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Polshyn, Hryhoriy, Tyler R. Naibert, and Raffi Budakian. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.184501.","ista":"Polshyn H, Naibert TR, Budakian R. 2018. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 97(18), 184501.","mla":"Polshyn, Hryhoriy, et al. “Imaging Phase Slip Dynamics in Micron-Size Superconducting Rings.” Physical Review B, vol. 97, no. 18, 184501, American Physical Society, 2018, doi:10.1103/physrevb.97.184501.","ama":"Polshyn H, Naibert TR, Budakian R. Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. 2018;97(18). doi:10.1103/physrevb.97.184501","apa":"Polshyn, H., Naibert, T. R., & Budakian, R. (2018). Imaging phase slip dynamics in micron-size superconducting rings. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.184501","short":"H. Polshyn, T.R. Naibert, R. Budakian, Physical Review B 97 (2018).","ieee":"H. Polshyn, T. R. Naibert, and R. Budakian, “Imaging phase slip dynamics in micron-size superconducting rings,” Physical Review B, vol. 97, no. 18. American Physical Society, 2018."},"article_number":"184501"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253."},"title":"Quasipolynomial set-based symbolic algorithms for parity games","article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","full_name":"Dvořák, Wolfgang","last_name":"Dvořák"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Alexander","full_name":"Svozil, Alexander","last_name":"Svozil"}],"project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","day":"23","year":"2018","has_accepted_license":"1","date_created":"2022-03-18T12:46:32Z","doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","page":"233-253","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","oa":1,"quality_controlled":"1","publisher":"EasyChair","ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","department":[{"_id":"KrCh"}],"file_date_updated":"2022-05-17T07:51:08Z","_id":"10883","status":"public","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Awassa, Ethiopia","end_date":"2018-11-21","start_date":"2018-11-17"},"type":"conference","language":[{"iso":"eng"}],"file":[{"file_size":720893,"date_updated":"2022-05-17T07:51:08Z","creator":"dernst","file_name":"2018_EPiCs_Chatterjee.pdf","date_created":"2022-05-17T07:51:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480"}],"publication_status":"published","publication_identifier":{"issn":["2398-7340"]},"ec_funded":1,"volume":57,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space."}],"intvolume":" 57","month":"10","scopus_import":"1","alternative_title":["EPiC Series in Computing"]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X.","ista":"Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93.","mla":"Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X.","apa":"Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X","ama":"Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X","ieee":"F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018.","short":"F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93."},"date_updated":"2021-01-12T06:48:13Z","title":"Generalized permutohedra from probabilistic graphical models","publist_id":"6284","author":[{"last_name":"Mohammadi","full_name":"Mohammadi, Fatemeh","first_name":"Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","full_name":"Wang, Charles","first_name":"Charles"},{"first_name":"Josephine","full_name":"Yu, Josephine","last_name":"Yu"}],"_id":"1092","status":"public","type":"journal_article","publication":"SIAM Journal on Discrete Mathematics","language":[{"iso":"eng"}],"day":"01","year":"2018","publication_status":"published","date_created":"2018-12-11T11:50:06Z","volume":32,"date_published":"2018-01-01T00:00:00Z","doi":"10.1137/16M107894X","issue":"1","page":"64-93","oa_version":"Preprint","abstract":[{"text":"A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. ","lang":"eng"}],"intvolume":" 32","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.01814"}],"publisher":"SIAM","quality_controlled":"1"},{"external_id":{"arxiv":["1806.10843"]},"author":[{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"}],"publist_id":"8045","title":"Mean-field limits of particles in interaction with quantised radiation fields","citation":{"mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"page":"185 - 214","date_created":"2018-12-11T11:44:08Z","doi":"10.1007/978-3-030-01602-9_9","date_published":"2018-10-27T00:00:00Z","year":"2018","day":"27","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:48:16Z","conference":{"end_date":"2017-04-01","location":"Munich, Germany","start_date":"2017-03-30","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"type":"conference","status":"public","_id":"11","ec_funded":1,"volume":270,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"scopus_import":1,"intvolume":" 270","month":"10","abstract":[{"text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.","lang":"eng"}],"oa_version":"Preprint"},{"year":"2018","publication":"Genes & Development","day":"18","page":"1321-1331","date_created":"2022-04-07T07:45:30Z","date_published":"2018-09-18T00:00:00Z","doi":"10.1101/gad.315523.118","oa":1,"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory","citation":{"short":"A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.","ieee":"A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.","apa":"McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118","ama":"McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118","mla":"McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.","ista":"McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.","chicago":"McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118."},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","article_processing_charge":"No","external_id":{"pmid":["30228202"]},"author":[{"first_name":"Asako","full_name":"McCloskey, Asako","last_name":"McCloskey"},{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"title":"Tpr regulates the total number of nuclear pore complexes per cell nucleus","publication_status":"published","publication_identifier":{"issn":["0890-9369","1549-5477"]},"language":[{"iso":"eng"}],"issue":"19-20","volume":32,"abstract":[{"text":"The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.315523.118"}],"scopus_import":"1","intvolume":" 32","month":"09","date_updated":"2022-07-18T08:32:32Z","extern":"1","_id":"11063","type":"journal_article","article_type":"original","keyword":["Developmental Biology","Genetics"],"status":"public"},{"extern":"1","date_updated":"2022-07-18T08:32:34Z","_id":"11064","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1474-760X"]},"volume":19,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.","lang":"eng"}],"intvolume":" 19","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-018-1599-6"}],"scopus_import":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6.","ista":"Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221.","mla":"Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6.","apa":"Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6","ama":"Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6","short":"J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018).","ieee":"J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018."},"title":"Predicting age from the transcriptome of human dermal fibroblasts","external_id":{"pmid":["30567591"]},"article_processing_charge":"No","author":[{"first_name":"Jason G.","last_name":"Fleischer","full_name":"Fleischer, Jason G."},{"first_name":"Roberta","full_name":"Schulte, Roberta","last_name":"Schulte"},{"last_name":"Tsai","full_name":"Tsai, Hsiao H.","first_name":"Hsiao H."},{"last_name":"Tyagi","full_name":"Tyagi, Swati","first_name":"Swati"},{"first_name":"Arkaitz","last_name":"Ibarra","full_name":"Ibarra, Arkaitz"},{"first_name":"Maxim N.","full_name":"Shokhirev, Maxim N.","last_name":"Shokhirev"},{"first_name":"Ling","full_name":"Huang, Ling","last_name":"Huang"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X","last_name":"HETZER"},{"last_name":"Navlakha","full_name":"Navlakha, Saket","first_name":"Saket"}],"article_number":"221","publication":"Genome Biology","day":"20","year":"2018","date_created":"2022-04-07T07:45:40Z","doi":"10.1186/s13059-018-1599-6","date_published":"2018-12-20T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"BioMed Central"}]