[{"article_type":"original","abstract":[{"text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.","lang":"eng"}],"day":"14","oa_version":"Submitted Version","volume":141,"quality_controlled":"1","external_id":{"pmid":["31199882"]},"date_updated":"2021-01-12T08:19:04Z","month":"06","title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","year":"2019","date_published":"2019-06-14T00:00:00Z","citation":{"ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","ieee":"D. F. Gauto <i>et al.</i>, “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:<a href=\"https://doi.org/10.1021/jacs.9b04219\">10.1021/jacs.9b04219</a>.","short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.9b04219\">https://doi.org/10.1021/jacs.9b04219</a>","ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. <i>Journal of the American Chemical Society</i>. 2019;141(28):11183-11195. doi:<a href=\"https://doi.org/10.1021/jacs.9b04219\">10.1021/jacs.9b04219</a>","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.9b04219\">https://doi.org/10.1021/jacs.9b04219</a>."},"publication_identifier":{"issn":["0002-7863","1520-5126"]},"publisher":"American Chemical Society","article_processing_charge":"No","doi":"10.1021/jacs.9b04219","publication_status":"published","pmid":1,"intvolume":"       141","page":"11183-11195","date_created":"2020-09-17T10:29:00Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"issue":"28","author":[{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"full_name":"Barducci, Alessandro","last_name":"Barducci","first_name":"Alessandro"},{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"last_name":"Terauchi","full_name":"Terauchi, Tsutomu","first_name":"Tsutomu"},{"full_name":"Gajan, David","last_name":"Gajan","first_name":"David"},{"first_name":"Yohei","full_name":"Miyanoiri, Yohei","last_name":"Miyanoiri"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman","first_name":"Roman"},{"full_name":"Kainosho, Masatsune","last_name":"Kainosho","first_name":"Masatsune"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","extern":"1","_id":"8408"},{"title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","date_updated":"2021-01-12T08:19:05Z","month":"04","publisher":"Elsevier","article_processing_charge":"No","publication_identifier":{"issn":["1047-8477"]},"doi":"10.1016/j.jsb.2018.07.009","publication_status":"published","year":"2019","date_published":"2019-04-01T00:00:00Z","citation":{"chicago":"Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” <i>Journal of Structural Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jsb.2018.07.009\">https://doi.org/10.1016/j.jsb.2018.07.009</a>.","ama":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. <i>Journal of Structural Biology</i>. 2019;206(1):66-72. doi:<a href=\"https://doi.org/10.1016/j.jsb.2018.07.009\">10.1016/j.jsb.2018.07.009</a>","apa":"Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., &#38; Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. <i>Journal of Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsb.2018.07.009\">https://doi.org/10.1016/j.jsb.2018.07.009</a>","short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","mla":"Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” <i>Journal of Structural Biology</i>, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:<a href=\"https://doi.org/10.1016/j.jsb.2018.07.009\">10.1016/j.jsb.2018.07.009</a>.","ieee":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” <i>Journal of Structural Biology</i>, vol. 206, no. 1. Elsevier, pp. 66–72, 2019.","ista":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72."},"article_type":"original","abstract":[{"text":"The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.","lang":"eng"}],"external_id":{"pmid":["30031884"]},"quality_controlled":"1","volume":206,"day":"01","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Waldemar","last_name":"Vollmer","full_name":"Vollmer, Waldemar"},{"first_name":"Jean-Pierre","last_name":"Simorre","full_name":"Simorre, Jean-Pierre"},{"last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"type":"journal_article","extern":"1","issue":"1","_id":"8409","page":"66-72","pmid":1,"intvolume":"       206","publication":"Journal of Structural Biology","language":[{"iso":"eng"}],"date_created":"2020-09-17T10:29:10Z","keyword":["Structural Biology"],"status":"public"},{"article_type":"letter_note","main_file_link":[{"url":"https://doi.org/10.1002/cphc.201801100","open_access":"1"}],"oa_version":"Published Version","day":"21","volume":20,"external_id":{"pmid":["30556633"]},"quality_controlled":"1","month":"01","date_updated":"2021-01-12T08:19:05Z","title":"NMR for Biological Systems","citation":{"short":"P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.","apa":"Schanda, P., &#38; Chekmenev, E. Y. (2019). NMR for Biological Systems. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201801100\">https://doi.org/10.1002/cphc.201801100</a>","ama":"Schanda P, Chekmenev EY. NMR for Biological Systems. <i>ChemPhysChem</i>. 2019;20(2):177-177. doi:<a href=\"https://doi.org/10.1002/cphc.201801100\">10.1002/cphc.201801100</a>","chicago":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201801100\">https://doi.org/10.1002/cphc.201801100</a>.","ista":"Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177.","ieee":"P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 177–177, 2019.","mla":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:<a href=\"https://doi.org/10.1002/cphc.201801100\">10.1002/cphc.201801100</a>."},"year":"2019","date_published":"2019-01-21T00:00:00Z","doi":"10.1002/cphc.201801100","publication_identifier":{"issn":["1439-4235"]},"article_processing_charge":"No","publisher":"Wiley","publication_status":"published","intvolume":"        20","pmid":1,"page":"177-177","date_created":"2020-09-17T10:29:26Z","status":"public","language":[{"iso":"eng"}],"publication":"ChemPhysChem","issue":"2","type":"journal_article","author":[{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"last_name":"Chekmenev","full_name":"Chekmenev, Eduard Y.","first_name":"Eduard Y."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","oa":1,"_id":"8410"},{"volume":20,"day":"21","oa_version":"Submitted Version","quality_controlled":"1","external_id":{"pmid":["30444575"]},"abstract":[{"text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.","lang":"eng"}],"article_type":"original","citation":{"ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284.","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:<a href=\"https://doi.org/10.1002/cphc.201800935\">10.1002/cphc.201800935</a>.","short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284.","apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., &#38; Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201800935\">https://doi.org/10.1002/cphc.201800935</a>","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. <i>ChemPhysChem</i>. 2019;20(2):276-284. doi:<a href=\"https://doi.org/10.1002/cphc.201800935\">10.1002/cphc.201800935</a>","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201800935\">https://doi.org/10.1002/cphc.201800935</a>."},"date_published":"2019-01-21T00:00:00Z","year":"2019","publication_status":"published","doi":"10.1002/cphc.201800935","article_processing_charge":"No","publisher":"Wiley","publication_identifier":{"issn":["1439-4235"]},"month":"01","date_updated":"2021-01-12T08:19:06Z","title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","date_created":"2020-09-17T10:29:36Z","status":"public","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"language":[{"iso":"eng"}],"publication":"ChemPhysChem","intvolume":"        20","pmid":1,"page":"276-284","_id":"8411","issue":"2","extern":"1","type":"journal_article","author":[{"full_name":"Marion, Dominique","last_name":"Marion","first_name":"Dominique"},{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"full_name":"Giandoreggio-Barranco, Karine","last_name":"Giandoreggio-Barranco","first_name":"Karine"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.1002/cphc.201800779","publication_identifier":{"issn":["1439-4235"]},"publisher":"Wiley","article_processing_charge":"No","publication_status":"published","citation":{"ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.","mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:<a href=\"https://doi.org/10.1002/cphc.201800779\">10.1002/cphc.201800779</a>.","ieee":"M. D. Shannon <i>et al.</i>, “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201800779\">https://doi.org/10.1002/cphc.201800779</a>","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201800779\">https://doi.org/10.1002/cphc.201800779</a>.","ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. <i>ChemPhysChem</i>. 2019;20(2):311-317. doi:<a href=\"https://doi.org/10.1002/cphc.201800779\">10.1002/cphc.201800779</a>"},"year":"2019","date_published":"2019-01-21T00:00:00Z","title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR","month":"01","date_updated":"2021-01-12T08:19:06Z","external_id":{"pmid":["30276945"]},"quality_controlled":"1","oa_version":"Submitted Version","volume":20,"day":"21","article_type":"original","abstract":[{"text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.","lang":"eng"}],"_id":"8412","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matthew D.","full_name":"Shannon, Matthew D.","last_name":"Shannon"},{"first_name":"Theint","full_name":"Theint, Theint","last_name":"Theint"},{"first_name":"Dwaipayan","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Dwaipayan"},{"first_name":"Krystyna","full_name":"Surewicz, Krystyna","last_name":"Surewicz"},{"full_name":"Surewicz, Witold K.","last_name":"Surewicz","first_name":"Witold K."},{"first_name":"Dominique","full_name":"Marion, Dominique","last_name":"Marion"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Jaroniec","full_name":"Jaroniec, Christopher P.","first_name":"Christopher P."}],"extern":"1","issue":"2","language":[{"iso":"eng"}],"publication":"ChemPhysChem","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"status":"public","date_created":"2020-09-17T10:29:43Z","intvolume":"        20","pmid":1,"page":"311-317"},{"extern":"1","type":"journal_article","author":[{"first_name":"Petra","full_name":"Rovó, Petra","last_name":"Rovó"},{"last_name":"Smith","full_name":"Smith, Colin A.","first_name":"Colin A."},{"first_name":"Diego","last_name":"Gauto","full_name":"Gauto, Diego"},{"last_name":"de Groot","full_name":"de Groot, Bert L.","first_name":"Bert L."},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"full_name":"Linser, Rasmus","last_name":"Linser","first_name":"Rasmus"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","_id":"8413","intvolume":"       141","pmid":1,"page":"858-869","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"date_created":"2020-09-17T10:29:50Z","status":"public","title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","month":"01","date_updated":"2021-01-12T08:19:07Z","publication_status":"published","doi":"10.1021/jacs.8b09258","publisher":"American Chemical Society","article_processing_charge":"No","publication_identifier":{"issn":["0002-7863","1520-5126"]},"citation":{"ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869.","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” <i>Journal of the American Chemical Society</i>, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019.","mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” <i>Journal of the American Chemical Society</i>, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:<a href=\"https://doi.org/10.1021/jacs.8b09258\">10.1021/jacs.8b09258</a>.","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869.","apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., &#38; Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.8b09258\">https://doi.org/10.1021/jacs.8b09258</a>","ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. <i>Journal of the American Chemical Society</i>. 2019;141(2):858-869. doi:<a href=\"https://doi.org/10.1021/jacs.8b09258\">10.1021/jacs.8b09258</a>","chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/jacs.8b09258\">https://doi.org/10.1021/jacs.8b09258</a>."},"year":"2019","date_published":"2019-01-08T00:00:00Z","abstract":[{"lang":"eng","text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains."}],"article_type":"original","external_id":{"pmid":["30620186"]},"quality_controlled":"1","oa_version":"Submitted Version","day":"08","volume":141},{"page":"1531-1575","intvolume":"       374","date_created":"2020-09-17T10:41:27Z","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"status":"public","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"issue":"3","author":[{"last_name":"Bálint","full_name":"Bálint, Péter","first_name":"Péter"},{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"last_name":"Leguil","full_name":"Leguil, Martin","first_name":"Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","extern":"1","oa":1,"arxiv":1,"_id":"8415","article_type":"original","abstract":[{"text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1809.08947","open_access":"1"}],"oa_version":"Preprint","day":"09","volume":374,"external_id":{"arxiv":["1809.08947"]},"quality_controlled":"1","date_updated":"2021-01-12T08:19:08Z","month":"05","title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","year":"2019","date_published":"2019-05-09T00:00:00Z","citation":{"chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00220-019-03448-x\">https://doi.org/10.1007/s00220-019-03448-x</a>.","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. <i>Communications in Mathematical Physics</i>. 2019;374(3):1531-1575. doi:<a href=\"https://doi.org/10.1007/s00220-019-03448-x\">10.1007/s00220-019-03448-x</a>","apa":"Bálint, P., De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03448-x\">https://doi.org/10.1007/s00220-019-03448-x</a>","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” <i>Communications in Mathematical Physics</i>, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:<a href=\"https://doi.org/10.1007/s00220-019-03448-x\">10.1007/s00220-019-03448-x</a>.","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” <i>Communications in Mathematical Physics</i>, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575."},"article_processing_charge":"No","publication_identifier":{"issn":["0010-3616","1432-0916"]},"publisher":"Springer Nature","doi":"10.1007/s00220-019-03448-x","publication_status":"published"},{"article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.09341"}],"abstract":[{"text":"In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.","lang":"eng"}],"oa_version":"Preprint","day":"01","volume":19,"external_id":{"arxiv":["1809.09341"]},"quality_controlled":"1","date_updated":"2021-01-12T08:19:08Z","month":"04","title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables","date_published":"2019-04-01T00:00:00Z","year":"2019","citation":{"chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” <i>Moscow Mathematical Journal</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">https://doi.org/10.17323/1609-4514-2019-19-2-307-327</a>.","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. <i>Moscow Mathematical Journal</i>. 2019;19(2):307-327. doi:<a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">10.17323/1609-4514-2019-19-2-307-327</a>","apa":"Huang, G., &#38; Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. <i>Moscow Mathematical Journal</i>. American Mathematical Society. <a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">https://doi.org/10.17323/1609-4514-2019-19-2-307-327</a>","short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.","mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” <i>Moscow Mathematical Journal</i>, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:<a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">10.17323/1609-4514-2019-19-2-307-327</a>.","ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” <i>Moscow Mathematical Journal</i>, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","ista":"Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327."},"publication_identifier":{"issn":["1609-4514"]},"article_processing_charge":"No","publisher":"American Mathematical Society","doi":"10.17323/1609-4514-2019-19-2-307-327","publication_status":"published","intvolume":"        19","page":"307-327","date_created":"2020-09-17T10:41:36Z","status":"public","publication":"Moscow Mathematical Journal","language":[{"iso":"eng"}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Huang","full_name":"Huang, Guan","first_name":"Guan"},{"full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628"}],"type":"journal_article","extern":"1","oa":1,"arxiv":1,"_id":"8416"},{"_id":"8418","oa":1,"type":"journal_article","author":[{"full_name":"Guardia, Marcel","last_name":"Guardia","first_name":"Marcel"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","last_name":"Kaloshin"},{"first_name":"Jianlu","last_name":"Zhang","full_name":"Zhang, Jianlu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","issue":"2","language":[{"iso":"eng"}],"publication":"Archive for Rational Mechanics and Analysis","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"status":"public","date_created":"2020-09-17T10:41:51Z","page":"799-836","intvolume":"       233","doi":"10.1007/s00205-019-01368-7","publication_identifier":{"issn":["0003-9527","1432-0673"]},"article_processing_charge":"No","publisher":"Springer Nature","publication_status":"published","citation":{"mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:<a href=\"https://doi.org/10.1007/s00205-019-01368-7\">10.1007/s00205-019-01368-7</a>.","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.","ista":"Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836.","chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00205-019-01368-7\">https://doi.org/10.1007/s00205-019-01368-7</a>.","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. <i>Archive for Rational Mechanics and Analysis</i>. 2019;233(2):799-836. doi:<a href=\"https://doi.org/10.1007/s00205-019-01368-7\">10.1007/s00205-019-01368-7</a>","apa":"Guardia, M., Kaloshin, V., &#38; Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-019-01368-7\">https://doi.org/10.1007/s00205-019-01368-7</a>","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836."},"year":"2019","date_published":"2019-03-12T00:00:00Z","title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem","month":"03","date_updated":"2021-01-12T08:19:09Z","quality_controlled":"1","day":"12","volume":233,"oa_version":"Published Version","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00205-019-01368-7"}],"abstract":[{"text":"For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0.","lang":"eng"}]},{"publication_status":"published","doi":"10.1134/S1560354719060017","article_processing_charge":"No","publisher":"Springer","citation":{"short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.","apa":"Chierchia, L., &#38; Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. <i>Regular and Chaotic Dynamics</i>. Springer. <a href=\"https://doi.org/10.1134/S1560354719060017\">https://doi.org/10.1134/S1560354719060017</a>","ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. <i>Regular and Chaotic Dynamics</i>. 2019;24:583–606. doi:<a href=\"https://doi.org/10.1134/S1560354719060017\">10.1134/S1560354719060017</a>","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” <i>Regular and Chaotic Dynamics</i>. Springer, 2019. <a href=\"https://doi.org/10.1134/S1560354719060017\">https://doi.org/10.1134/S1560354719060017</a>.","ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606.","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” <i>Regular and Chaotic Dynamics</i>, vol. 24. Springer, pp. 583–606, 2019.","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” <i>Regular and Chaotic Dynamics</i>, vol. 24, Springer, 2019, pp. 583–606, doi:<a href=\"https://doi.org/10.1134/S1560354719060017\">10.1134/S1560354719060017</a>."},"date_published":"2019-12-10T00:00:00Z","year":"2019","title":"V. I. Arnold’s “pointwise” KAM theorem","month":"12","date_updated":"2021-01-12T08:20:34Z","quality_controlled":"1","external_id":{"arxiv":["1908.02523"]},"oa_version":"Preprint","day":"10","volume":24,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.02523"}],"abstract":[{"text":"We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed.","lang":"eng"}],"article_type":"original","_id":"8693","arxiv":1,"oa":1,"extern":"1","type":"journal_article","author":[{"last_name":"Chierchia","full_name":"Chierchia, Luigi","first_name":"Luigi"},{"first_name":"Edmond","orcid":"0000-0003-2640-4049","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","full_name":"Koudjinan, Edmond","last_name":"Koudjinan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Regular and Chaotic Dynamics","date_created":"2020-10-21T15:25:45Z","status":"public","page":"583–606","intvolume":"        24"},{"_id":"9016","oa":1,"extern":"1","author":[{"last_name":"Bakail","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","first_name":"May M"},{"full_name":"Rodriguez‐Marin, Silvia","last_name":"Rodriguez‐Marin","first_name":"Silvia"},{"first_name":"Zsófia","full_name":"Hegedüs, Zsófia","last_name":"Hegedüs"},{"last_name":"Perrin","full_name":"Perrin, Marie E.","first_name":"Marie E."},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"},{"last_name":"Wilson","full_name":"Wilson, Andrew J.","first_name":"Andrew J."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"7","publication":"ChemBioChem","language":[{"iso":"eng"}],"date_created":"2021-01-19T10:59:14Z","status":"public","intvolume":"        20","page":"891-895","publication_status":"published","publication_identifier":{"issn":["1439-4227","1439-7633"]},"article_processing_charge":"No","publisher":"Wiley","doi":"10.1002/cbic.201800633","year":"2019","date_published":"2019-04-01T00:00:00Z","citation":{"ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” <i>ChemBioChem</i>, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>.","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. 2019;20(7):891-895. doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., &#38; Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>"},"title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","date_updated":"2023-02-23T13:46:48Z","month":"04","quality_controlled":"1","day":"01","oa_version":"Published Version","volume":20,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1002/cbic.201800633"}],"abstract":[{"lang":"eng","text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs."}],"article_type":"original"},{"pmid":1,"page":"1573-1585.e10","intvolume":"        26","date_created":"2021-01-19T11:04:50Z","status":"public","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"language":[{"iso":"eng"}],"publication":"Cell Chemical Biology","issue":"11","type":"journal_article","author":[{"first_name":"May M","orcid":"0000-0002-9592-1587","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","full_name":"Bakail, May M","last_name":"Bakail"},{"first_name":"Albane","full_name":"Gaubert, Albane","last_name":"Gaubert"},{"full_name":"Andreani, Jessica","last_name":"Andreani","first_name":"Jessica"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"last_name":"Pinna","full_name":"Pinna, Guillaume","first_name":"Guillaume"},{"first_name":"Ekaterina","full_name":"Boyarchuk, Ekaterina","last_name":"Boyarchuk"},{"full_name":"Gaillard, Marie-Cécile","last_name":"Gaillard","first_name":"Marie-Cécile"},{"first_name":"Regis","full_name":"Courbeyrette, Regis","last_name":"Courbeyrette"},{"full_name":"Mann, Carl","last_name":"Mann","first_name":"Carl"},{"first_name":"Jean-Yves","last_name":"Thuret","full_name":"Thuret, Jean-Yves"},{"first_name":"Bérengère","full_name":"Guichard, Bérengère","last_name":"Guichard"},{"last_name":"Murciano","full_name":"Murciano, Brice","first_name":"Brice"},{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"first_name":"Adeline","last_name":"Poitou","full_name":"Poitou, Adeline"},{"first_name":"Claire","full_name":"Frederic, Claire","last_name":"Frederic"},{"full_name":"Le Du, Marie-Hélène","last_name":"Le Du","first_name":"Marie-Hélène"},{"first_name":"Morgane","full_name":"Agez, Morgane","last_name":"Agez"},{"full_name":"Roelants, Caroline","last_name":"Roelants","first_name":"Caroline"},{"first_name":"Zachary A.","last_name":"Gurard-Levin","full_name":"Gurard-Levin, Zachary A."},{"first_name":"Geneviève","last_name":"Almouzni","full_name":"Almouzni, Geneviève"},{"last_name":"Cherradi","full_name":"Cherradi, Nadia","first_name":"Nadia"},{"full_name":"Guerois, Raphael","last_name":"Guerois","first_name":"Raphael"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","oa":1,"_id":"9018","article_type":"original","abstract":[{"text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chembiol.2019.09.002"}],"volume":26,"oa_version":"Published Version","day":"21","quality_controlled":"1","external_id":{"pmid":["31543461"]},"month":"11","date_updated":"2023-02-23T13:46:53Z","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","citation":{"ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>.","ieee":"M. M. Bakail <i>et al.</i>, “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” <i>Cell Chemical Biology</i>, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>.","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. 2019;26(11):1573-1585.e10. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>"},"year":"2019","date_published":"2019-11-21T00:00:00Z","doi":"10.1016/j.chembiol.2019.09.002","article_processing_charge":"No","publication_identifier":{"issn":["2451-9456"]},"publisher":"Elsevier","publication_status":"published"},{"ddc":["530"],"file":[{"date_created":"2021-02-02T13:47:21Z","checksum":"70c6e5d6fbea0932b0669505ab6633ec","access_level":"open_access","success":1,"file_size":2820337,"relation":"main_file","date_updated":"2021-02-02T13:47:21Z","file_name":"2019_NatureComm_Ramananarivo.pdf","content_type":"application/pdf","file_id":"9061","creator":"cziletti"}],"intvolume":"        10","pmid":1,"scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_created":"2021-02-02T13:43:36Z","status":"public","publication":"Nature Communications","language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"1","file_date_updated":"2021-02-02T13:47:21Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","author":[{"first_name":"Sophie","full_name":"Ramananarivo, Sophie","last_name":"Ramananarivo"},{"first_name":"Etienne","full_name":"Ducrot, Etienne","last_name":"Ducrot"},{"orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A","last_name":"Palacci"}],"type":"journal_article","extern":"1","oa":1,"arxiv":1,"_id":"9060","article_type":"original","abstract":[{"text":"Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium.","lang":"eng"}],"volume":10,"day":"29","oa_version":"Published Version","quality_controlled":"1","external_id":{"pmid":["31358762"],"arxiv":["1909.07382"]},"date_updated":"2023-02-23T13:47:59Z","month":"07","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_number":"3380","title":"Activity-controlled annealing of colloidal monolayers","year":"2019","date_published":"2019-07-29T00:00:00Z","citation":{"ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>.","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","apa":"Ramananarivo, S., Ducrot, E., &#38; Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-11362-y\">https://doi.org/10.1038/s41467-019-11362-y</a>.","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-11362-y\">10.1038/s41467-019-11362-y</a>"},"publication_identifier":{"issn":["2041-1723"]},"publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41467-019-11362-y","publication_status":"published"},{"page":"509-515","conference":{"start_date":"2019-10-07","location":"Barcelona, Spain","name":"IASS: International Association for Shell and Spatial Structures","end_date":"2019-10-10"},"abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","language":[{"iso":"eng"}],"external_id":{"isi":["000563497600059"]},"quality_controlled":"1","scopus_import":"1","status":"public","date_created":"2021-03-21T23:01:21Z","day":"10","oa_version":"None","isi":1,"author":[{"last_name":"Laccone","full_name":"Laccone, Francesco","first_name":"Francesco"},{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus","first_name":"Jesus"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"},{"first_name":"Federico","full_name":"Ponchio, Federico","last_name":"Ponchio"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","date_updated":"2023-09-08T11:21:54Z","month":"10","department":[{"_id":"BeBi"}],"publication_identifier":{"isbn":["9788412110104"],"issn":["2518-6582"]},"article_processing_charge":"No","publisher":"International Center for Numerical Methods in Engineering","_id":"9261","publication_status":"published","date_published":"2019-10-10T00:00:00Z","year":"2019","citation":{"mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","ieee":"F. Laccone <i>et al.</i>, “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, Barcelona, Spain, 2019, pp. 509–515.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.","chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>, 509–15. International Center for Numerical Methods in Engineering, 2019.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i>. International Center for Numerical Methods in Engineering; 2019:509-515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., &#38; Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In <i>IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE</i> (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515."}},{"status":"public","keyword":["Multidisciplinary"],"scopus_import":"1","date_created":"2021-06-04T12:38:20Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","ddc":["580"],"file":[{"file_id":"9461","creator":"asandaue","content_type":"application/pdf","file_name":"2019_PNAS_Kim.pdf","date_updated":"2021-06-04T12:50:47Z","relation":"main_file","file_size":1142540,"access_level":"open_access","success":1,"checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","date_created":"2021-06-04T12:50:47Z"}],"pmid":1,"intvolume":"       116","page":"9652-9657","oa":1,"_id":"9460","issue":"19","file_date_updated":"2021-06-04T12:50:47Z","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"full_name":"Ono, Akemi","last_name":"Ono","first_name":"Akemi"},{"full_name":"Scholten, Stefan","last_name":"Scholten","first_name":"Stefan"},{"first_name":"Tetsu","full_name":"Kinoshita, Tetsu","last_name":"Kinoshita"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"extern":"1","oa_version":"Published Version","volume":116,"day":"07","external_id":{"pmid":["31000601"]},"quality_controlled":"1","article_type":"original","abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"citation":{"mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>.","ieee":"M. Y. Kim <i>et al.</i>, “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>.","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. 2019;116(19):9652-9657. doi:<a href=\"https://doi.org/10.1073/pnas.1821435116\">10.1073/pnas.1821435116</a>","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., &#38; Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1821435116\">https://doi.org/10.1073/pnas.1821435116</a>","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657."},"year":"2019","date_published":"2019-05-07T00:00:00Z","doi":"10.1073/pnas.1821435116","publisher":"National Academy of Sciences","article_processing_charge":"No","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","department":[{"_id":"DaZi"}],"month":"05","date_updated":"2021-12-14T07:52:30Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm"},{"article_type":"original","abstract":[{"lang":"eng","text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems."}],"quality_controlled":"1","external_id":{"pmid":["31601251"]},"oa_version":"Published Version","day":"10","volume":12,"article_number":"62","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","department":[{"_id":"DaZi"}],"month":"10","date_updated":"2021-12-14T07:53:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1186/s13072-019-0307-4","article_processing_charge":"No","publisher":"Springer Nature","publication_identifier":{"eissn":["1756-8935"]},"publication_status":"published","citation":{"apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., &#38; Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s13072-019-0307-4\">https://doi.org/10.1186/s13072-019-0307-4</a>.","ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. <i>Epigenetics and Chromatin</i>. 2019;12. doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” <i>Epigenetics and Chromatin</i>, vol. 12, 62, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s13072-019-0307-4\">10.1186/s13072-019-0307-4</a>.","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” <i>Epigenetics and Chromatin</i>, vol. 12. Springer Nature, 2019."},"date_published":"2019-10-10T00:00:00Z","year":"2019","pmid":1,"intvolume":"        12","ddc":["570"],"file":[{"file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","date_updated":"2021-06-08T09:29:19Z","content_type":"application/pdf","file_id":"9531","creator":"asandaue","date_created":"2021-06-08T09:29:19Z","checksum":"86ff50a7517891511af2733c76c81b67","success":1,"access_level":"open_access","relation":"main_file","file_size":3221067}],"language":[{"iso":"eng"}],"publication":"Epigenetics and Chromatin","has_accepted_license":"1","scopus_import":"1","status":"public","date_created":"2021-06-08T09:21:51Z","type":"journal_article","author":[{"first_name":"Keith D.","last_name":"Harris","full_name":"Harris, Keith D."},{"first_name":"James P. B.","last_name":"Lloyd","full_name":"Lloyd, James P. B."},{"last_name":"Domb","full_name":"Domb, Katherine","first_name":"Katherine"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","file_date_updated":"2021-06-08T09:29:19Z","_id":"9530","oa":1},{"arxiv":1,"_id":"9580","oa":1,"type":"journal_article","author":[{"last_name":"Conlon","full_name":"Conlon, David","first_name":"David"},{"last_name":"Fox","full_name":"Fox, Jacob","first_name":"Jacob"},{"full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"first_name":"Benny","last_name":"Sudakov","full_name":"Sudakov, Benny"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","extern":"1","issue":"1","language":[{"iso":"eng"}],"publication":"Israel Journal of Mathematics","scopus_import":"1","status":"public","date_created":"2021-06-21T13:36:02Z","intvolume":"       233","page":"67-111","doi":"10.1007/s11856-019-1897-z","publisher":"Springer","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]},"article_processing_charge":"No","publication_status":"published","citation":{"ista":"Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111.","ieee":"D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” <i>Israel Journal of Mathematics</i>, vol. 233, no. 1. Springer, pp. 67–111, 2019.","mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” <i>Israel Journal of Mathematics</i>, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:<a href=\"https://doi.org/10.1007/s11856-019-1897-z\">10.1007/s11856-019-1897-z</a>.","short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","apa":"Conlon, D., Fox, J., Kwan, M. A., &#38; Sudakov, B. (2019). Hypergraph cuts above the average. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-019-1897-z\">https://doi.org/10.1007/s11856-019-1897-z</a>","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. <i>Israel Journal of Mathematics</i>. 2019;233(1):67-111. doi:<a href=\"https://doi.org/10.1007/s11856-019-1897-z\">10.1007/s11856-019-1897-z</a>","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” <i>Israel Journal of Mathematics</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11856-019-1897-z\">https://doi.org/10.1007/s11856-019-1897-z</a>."},"date_published":"2019-08-01T00:00:00Z","year":"2019","title":"Hypergraph cuts above the average","month":"08","date_updated":"2023-02-23T14:01:41Z","quality_controlled":"1","external_id":{"arxiv":["1803.08462"]},"volume":233,"day":"01","oa_version":"Preprint","article_type":"original","abstract":[{"lang":"eng","text":"An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation."}],"main_file_link":[{"url":"https://arxiv.org/abs/1803.08462","open_access":"1"}]},{"oa":1,"arxiv":1,"_id":"9585","issue":"8","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","last_name":"Kwan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"}],"type":"journal_article","extern":"1","date_created":"2021-06-22T09:31:45Z","status":"public","scopus_import":"1","publication":"Transactions of the American Mathematical Society","language":[{"iso":"eng"}],"page":"5571-5594","intvolume":"       372","year":"2019","date_published":"2019-10-15T00:00:00Z","citation":{"ista":"Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” <i>Transactions of the American Mathematical Society</i>, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:<a href=\"https://doi.org/10.1090/tran/7729\">10.1090/tran/7729</a>.","ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” <i>Transactions of the American Mathematical Society</i>, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","apa":"Kwan, M. A., &#38; Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/7729\">https://doi.org/10.1090/tran/7729</a>","short":"M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594.","chicago":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.1090/tran/7729\">https://doi.org/10.1090/tran/7729</a>.","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. <i>Transactions of the American Mathematical Society</i>. 2019;372(8):5571-5594. doi:<a href=\"https://doi.org/10.1090/tran/7729\">10.1090/tran/7729</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"publisher":"American Mathematical Society","doi":"10.1090/tran/7729","publication_status":"published","date_updated":"2023-02-23T14:01:50Z","month":"10","title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","volume":372,"oa_version":"Submitted Version","day":"15","quality_controlled":"1","external_id":{"arxiv":["1712.05656"]},"article_type":"original","abstract":[{"lang":"eng","text":"An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture."}],"main_file_link":[{"url":"https://doi.org/10.1090/tran/7729","open_access":"1"}]},{"issue":"3","author":[{"last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"last_name":"Sudakov","full_name":"Sudakov, Benny","first_name":"Benny"},{"first_name":"Tuan","last_name":"Tran","full_name":"Tran, Tuan"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"journal_article","extern":"1","oa":1,"arxiv":1,"_id":"9586","page":"757-777","intvolume":"        99","date_created":"2021-06-22T09:46:03Z","scopus_import":"1","status":"public","publication":"Journal of the London Mathematical Society","language":[{"iso":"eng"}],"date_updated":"2023-02-23T14:01:53Z","month":"05","title":"Anticoncentration for subgraph statistics","date_published":"2019-05-03T00:00:00Z","year":"2019","citation":{"mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:<a href=\"https://doi.org/10.1112/jlms.12192\">10.1112/jlms.12192</a>.","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 757–777, 2019.","ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777.","chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12192\">https://doi.org/10.1112/jlms.12192</a>.","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. <i>Journal of the London Mathematical Society</i>. 2019;99(3):757-777. doi:<a href=\"https://doi.org/10.1112/jlms.12192\">10.1112/jlms.12192</a>","apa":"Kwan, M. A., Sudakov, B., &#38; Tran, T. (2019). Anticoncentration for subgraph statistics. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12192\">https://doi.org/10.1112/jlms.12192</a>","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777."},"publisher":"Wiley","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"article_processing_charge":"No","doi":"10.1112/jlms.12192","publication_status":"published","article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05202"}],"abstract":[{"text":"Consider integers  𝑘,ℓ  such that  0⩽ℓ⩽(𝑘2) . Given a large graph  𝐺 , what is the fraction of  𝑘 -vertex subsets of  𝐺  which span exactly  ℓ  edges? When  𝐺  is empty or complete, and  ℓ  is zero or  (𝑘2) , this fraction can be exactly 1. On the other hand, if  ℓ  is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet  ℓ∗=min{ℓ,(𝑘2)−ℓ} . Our main result is that for any  𝑘  and  ℓ , the fraction of  𝑘 -vertex subsets that span  ℓ  edges is at most  log𝑂(1)(ℓ∗/𝑘)√ 𝑘/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube.","lang":"eng"}],"oa_version":"Preprint","day":"03","volume":99,"quality_controlled":"1","external_id":{"arxiv":["1807.05202"]}},{"extern":"1","type":"journal_article","author":[{"full_name":"Kapil, Venkat","last_name":"Kapil","first_name":"Venkat"},{"first_name":"Mariana","full_name":"Rossi, Mariana","last_name":"Rossi"},{"first_name":"Ondrej","last_name":"Marsalek","full_name":"Marsalek, Ondrej"},{"last_name":"Petraglia","full_name":"Petraglia, Riccardo","first_name":"Riccardo"},{"first_name":"Yair","full_name":"Litman, Yair","last_name":"Litman"},{"last_name":"Spura","full_name":"Spura, Thomas","first_name":"Thomas"},{"first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing"},{"first_name":"Alice","last_name":"Cuzzocrea","full_name":"Cuzzocrea, Alice"},{"first_name":"Robert H.","last_name":"Meißner","full_name":"Meißner, Robert H."},{"first_name":"David M.","last_name":"Wilkins","full_name":"Wilkins, David M."},{"full_name":"Helfrecht, Benjamin A.","last_name":"Helfrecht","first_name":"Benjamin A."},{"first_name":"Przemysław","full_name":"Juda, Przemysław","last_name":"Juda"},{"full_name":"Bienvenue, Sébastien P.","last_name":"Bienvenue","first_name":"Sébastien P."},{"first_name":"Wei","full_name":"Fang, Wei","last_name":"Fang"},{"first_name":"Jan","last_name":"Kessler","full_name":"Kessler, Jan"},{"first_name":"Igor","last_name":"Poltavsky","full_name":"Poltavsky, Igor"},{"first_name":"Steven","last_name":"Vandenbrande","full_name":"Vandenbrande, Steven"},{"last_name":"Wieme","full_name":"Wieme, Jelle","first_name":"Jelle"},{"first_name":"Clemence","last_name":"Corminboeuf","full_name":"Corminboeuf, Clemence"},{"first_name":"Thomas D.","full_name":"Kühne, Thomas D.","last_name":"Kühne"},{"first_name":"David E.","last_name":"Manolopoulos","full_name":"Manolopoulos, David E."},{"full_name":"Markland, Thomas E.","last_name":"Markland","first_name":"Thomas E."},{"first_name":"Jeremy O.","full_name":"Richardson, Jeremy O.","last_name":"Richardson"},{"first_name":"Alexandre","last_name":"Tkatchenko","full_name":"Tkatchenko, Alexandre"},{"last_name":"Tribello","full_name":"Tribello, Gareth A.","first_name":"Gareth A."},{"first_name":"Veronique","last_name":"Van Speybroeck","full_name":"Van Speybroeck, Veronique"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9677","arxiv":1,"oa":1,"intvolume":"       236","page":"214-223","language":[{"iso":"eng"}],"publication":"Computer Physics Communications","date_created":"2021-07-16T08:53:01Z","status":"public","scopus_import":"1","title":"i-PI 2.0: A universal force engine for advanced molecular simulations","month":"03","date_updated":"2021-08-09T12:37:16Z","publication_status":"published","doi":"10.1016/j.cpc.2018.09.020","publisher":"Elsevier","article_processing_charge":"No","publication_identifier":{"issn":["0010-4655"]},"citation":{"chicago":"Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” <i>Computer Physics Communications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">https://doi.org/10.1016/j.cpc.2018.09.020</a>.","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. <i>Computer Physics Communications</i>. 2019;236:214-223. doi:<a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">10.1016/j.cpc.2018.09.020</a>","apa":"Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. <i>Computer Physics Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">https://doi.org/10.1016/j.cpc.2018.09.020</a>","short":"V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223.","mla":"Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” <i>Computer Physics Communications</i>, vol. 236, Elsevier, 2019, pp. 214–23, doi:<a href=\"https://doi.org/10.1016/j.cpc.2018.09.020\">10.1016/j.cpc.2018.09.020</a>.","ieee":"V. Kapil <i>et al.</i>, “i-PI 2.0: A universal force engine for advanced molecular simulations,” <i>Computer Physics Communications</i>, vol. 236. Elsevier, pp. 214–223, 2019.","ista":"Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223."},"year":"2019","date_published":"2019-03-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1808.03824","open_access":"1"}],"abstract":[{"text":"Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.","lang":"eng"}],"article_type":"original","quality_controlled":"1","external_id":{"arxiv":["1808.03824"]},"day":"01","oa_version":"Preprint","volume":236}]