[{"main_file_link":[{"url":"https://arxiv.org/abs/1809.08947","open_access":"1"}],"status":"public","citation":{"chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x.","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","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.","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","apa":"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. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x"},"arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","month":"05","publication_status":"published","day":"09","doi":"10.1007/s00220-019-03448-x","type":"journal_article","date_updated":"2021-01-12T08:19:08Z","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"}],"publication":"Communications in Mathematical Physics","date_created":"2020-09-17T10:41:27Z","publication_identifier":{"issn":["0010-3616","1432-0916"]},"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"oa":1,"article_type":"original","title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publisher":"Springer Nature","article_processing_charge":"No","page":"1531-1575","date_published":"2019-05-09T00:00:00Z","volume":374,"intvolume":" 374","author":[{"last_name":"Bálint","full_name":"Bálint, Péter","first_name":"Péter"},{"first_name":"Jacopo","full_name":"De Simoi, Jacopo","last_name":"De Simoi"},{"first_name":"Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"},{"full_name":"Leguil, Martin","last_name":"Leguil","first_name":"Martin"}],"issue":"3","_id":"8415","extern":"1","external_id":{"arxiv":["1809.08947"]}},{"oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables","type":"journal_article","date_updated":"2021-01-12T08:19:08Z","abstract":[{"lang":"eng","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."}],"date_created":"2020-09-17T10:41:36Z","publication":"Moscow Mathematical Journal","publication_identifier":{"issn":["1609-4514"]},"arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","month":"04","publication_status":"published","day":"01","doi":"10.17323/1609-4514-2019-19-2-307-327","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1809.09341","open_access":"1"}],"citation":{"ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” Moscow Mathematical Journal, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","apa":"Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327","short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.","chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327.","mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:10.17323/1609-4514-2019-19-2-307-327.","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."},"author":[{"full_name":"Huang, Guan","last_name":"Huang","first_name":"Guan"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim"}],"_id":"8416","extern":"1","issue":"2","external_id":{"arxiv":["1809.09341"]},"volume":19,"intvolume":" 19","article_processing_charge":"No","page":"307-327","date_published":"2019-04-01T00:00:00Z","year":"2019","publisher":"American Mathematical Society"},{"date_updated":"2021-01-12T08:19:09Z","type":"journal_article","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_identifier":{"issn":["0003-9527","1432-0673"]},"date_created":"2020-09-17T10:41:51Z","publication":"Archive for Rational Mechanics and Analysis","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"oa":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem","main_file_link":[{"url":"https://doi.org/10.1007/s00205-019-01368-7","open_access":"1"}],"status":"public","citation":{"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.","mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7.","chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7.","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836.","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7","apa":"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. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019."},"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"month":"03","doi":"10.1007/s00205-019-01368-7","day":"12","publication_status":"published","volume":233,"intvolume":" 233","author":[{"first_name":"Marcel","last_name":"Guardia","full_name":"Guardia, Marcel"},{"orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Jianlu","last_name":"Zhang","full_name":"Zhang, Jianlu"}],"_id":"8418","extern":"1","issue":"2","year":"2019","publisher":"Springer Nature","article_processing_charge":"No","page":"799-836","date_published":"2019-03-12T00:00:00Z"},{"corr_author":"1","month":"05","day":"25","doi":"10.29007/bj1w","department":[{"_id":"ToHe"}],"publication_status":"published","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"status":"public","citation":{"chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w"},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","conference":{"end_date":"2019-04-15","location":"Montreal, Canada","start_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"oa":1,"abstract":[{"lang":"eng","text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date."}],"publication_identifier":{"eissn":["2398-7340"]},"date_created":"2020-09-26T14:23:54Z","publication":"EPiC Series in Computing","date_updated":"2026-06-18T19:33:41Z","type":"conference","date_published":"2019-05-25T00:00:00Z","article_processing_charge":"No","page":"14-40","publisher":"EasyChair","ddc":["000"],"year":"2019","_id":"8570","author":[{"first_name":"Matthias","last_name":"Althoff","full_name":"Althoff, Matthias"},{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"first_name":"Marcelo","last_name":"Forets","full_name":"Forets, Marcelo"},{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"last_name":"Kochdumper","full_name":"Kochdumper, Niklas","first_name":"Niklas"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","orcid":"0000-0003-3658-1065","first_name":"Christian"},{"first_name":"Stefan","full_name":"Schupp, Stefan","last_name":"Schupp"}],"intvolume":" 61","volume":61},{"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"}],"publication":"Regular and Chaotic Dynamics","date_created":"2020-10-21T15:25:45Z","type":"journal_article","date_updated":"2021-01-12T08:20:34Z","article_type":"original","title":"V. I. Arnold’s “pointwise” KAM theorem","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.02523"}],"citation":{"ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017","apa":"Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.","ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606.","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.","short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017."},"month":"12","publication_status":"published","day":"10","doi":"10.1134/S1560354719060017","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","intvolume":" 24","volume":24,"external_id":{"arxiv":["1908.02523"]},"_id":"8693","extern":"1","author":[{"full_name":"Chierchia, Luigi","last_name":"Chierchia","first_name":"Luigi"},{"last_name":"Koudjinan","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","orcid":"0000-0003-2640-4049","first_name":"Edmond"}],"publisher":"Springer","year":"2019","date_published":"2019-12-10T00:00:00Z","article_processing_charge":"No","page":"583–606"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","article_type":"original","oa":1,"publication":"ChemBioChem","date_created":"2021-01-19T10:59:14Z","publication_identifier":{"issn":["1439-4227","1439-7633"]},"abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_updated":"2023-02-23T13:46:48Z","publication_status":"published","day":"01","doi":"10.1002/cbic.201800633","month":"04","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","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,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633","ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633","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.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","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."},"status":"public","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1002/cbic.201800633"}],"_id":"9016","extern":"1","issue":"7","author":[{"orcid":"0000-0002-9592-1587","first_name":"May M","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","last_name":"Bakail"},{"first_name":"Silvia","full_name":"Rodriguez‐Marin, Silvia","last_name":"Rodriguez‐Marin"},{"first_name":"Zsófia","full_name":"Hegedüs, Zsófia","last_name":"Hegedüs"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"},{"first_name":"Andrew J.","full_name":"Wilson, Andrew J.","last_name":"Wilson"}],"intvolume":" 20","volume":20,"date_published":"2019-04-01T00:00:00Z","page":"891-895","article_processing_charge":"No","publisher":"Wiley","year":"2019"},{"volume":26,"intvolume":" 26","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","last_name":"Gaubert","full_name":"Gaubert, Albane"},{"first_name":"Jessica","last_name":"Andreani","full_name":"Andreani, Jessica"},{"first_name":"Gwenaëlle","full_name":"Moal, Gwenaëlle","last_name":"Moal"},{"full_name":"Pinna, Guillaume","last_name":"Pinna","first_name":"Guillaume"},{"full_name":"Boyarchuk, Ekaterina","last_name":"Boyarchuk","first_name":"Ekaterina"},{"first_name":"Marie-Cécile","last_name":"Gaillard","full_name":"Gaillard, Marie-Cécile"},{"full_name":"Courbeyrette, Regis","last_name":"Courbeyrette","first_name":"Regis"},{"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"},{"full_name":"Murciano, Brice","last_name":"Murciano","first_name":"Brice"},{"first_name":"Nicolas","full_name":"Richet, Nicolas","last_name":"Richet"},{"first_name":"Adeline","full_name":"Poitou, Adeline","last_name":"Poitou"},{"first_name":"Claire","full_name":"Frederic, Claire","last_name":"Frederic"},{"last_name":"Le Du","full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène"},{"first_name":"Morgane","last_name":"Agez","full_name":"Agez, Morgane"},{"full_name":"Roelants, Caroline","last_name":"Roelants","first_name":"Caroline"},{"first_name":"Zachary A.","full_name":"Gurard-Levin, Zachary A.","last_name":"Gurard-Levin"},{"last_name":"Almouzni","full_name":"Almouzni, Geneviève","first_name":"Geneviève"},{"last_name":"Cherradi","full_name":"Cherradi, Nadia","first_name":"Nadia"},{"last_name":"Guerois","full_name":"Guerois, Raphael","first_name":"Raphael"},{"first_name":"Françoise","full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein"}],"issue":"11","_id":"9018","extern":"1","external_id":{"pmid":["31543461"]},"year":"2019","publisher":"Elsevier","article_processing_charge":"No","page":"1573-1585.e10","pmid":1,"date_published":"2019-11-21T00:00:00Z","type":"journal_article","date_updated":"2023-02-23T13:46:53Z","abstract":[{"lang":"eng","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."}],"publication":"Cell Chemical Biology","date_created":"2021-01-19T11:04:50Z","publication_identifier":{"issn":["2451-9456"]},"keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"oa":1,"article_type":"original","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"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.","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.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.","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.","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. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002","ieee":"M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019."},"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","month":"11","publication_status":"published","doi":"10.1016/j.chembiol.2019.09.002","day":"21"},{"pmid":1,"date_published":"2019-07-29T00:00:00Z","article_processing_charge":"No","ddc":["530"],"publisher":"Springer Nature","year":"2019","article_number":"3380","_id":"9060","external_id":{"pmid":["31358762"],"arxiv":["1909.07382"]},"issue":"1","extern":"1","author":[{"last_name":"Ramananarivo","full_name":"Ramananarivo, Sophie","first_name":"Sophie"},{"first_name":"Etienne","last_name":"Ducrot","full_name":"Ducrot, Etienne"},{"full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","orcid":"0000-0002-7253-9465","first_name":"Jérémie A"}],"intvolume":" 10","volume":10,"publication_status":"published","doi":"10.1038/s41467-019-11362-y","day":"29","month":"07","quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"creator":"cziletti","file_size":2820337,"date_updated":"2021-02-02T13:47:21Z","file_name":"2019_NatureComm_Ramananarivo.pdf","date_created":"2021-02-02T13:47:21Z","file_id":"9061","checksum":"70c6e5d6fbea0932b0669505ab6633ec","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1}],"citation":{"chicago":"Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y.","mla":"Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.","short":"S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).","ista":"Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380.","ieee":"S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019.","apa":"Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y","ama":"Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y"},"status":"public","scopus_import":"1","title":"Activity-controlled annealing of colloidal monolayers","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","article_type":"original","has_accepted_license":"1","oa":1,"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_created":"2021-02-02T13:43:36Z","publication":"Nature Communications","publication_identifier":{"issn":["2041-1723"]},"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"}],"type":"journal_article","date_updated":"2023-02-23T13:47:59Z","file_date_updated":"2021-02-02T13:47:21Z"},{"month":"10","date_published":"2019-10-10T00:00:00Z","publication_status":"published","department":[{"_id":"BeBi"}],"day":"10","article_processing_charge":"No","quality_controlled":"1","page":"509-515","language":[{"iso":"eng"}],"oa_version":"None","status":"public","publisher":"International Center for Numerical Methods in Engineering","citation":{"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 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, 509–15. International Center for Numerical Methods in Engineering, 2019.","mla":"Laccone, Francesco, et al. “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, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","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.","apa":"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. 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 (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. 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; 2019:509-515.","ieee":"F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” 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, Barcelona, Spain, 2019, pp. 509–515."},"year":"2019","scopus_import":"1","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000563497600059"]},"_id":"9261","author":[{"last_name":"Laccone","full_name":"Laccone, Francesco","first_name":"Francesco"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus","last_name":"Perez Rodriguez"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"last_name":"Ponchio","full_name":"Ponchio, Federico","first_name":"Federico"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"isi":1,"conference":{"name":"IASS: International Association for Shell and Spatial Structures","start_date":"2019-10-07","location":"Barcelona, Spain","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"}],"date_created":"2021-03-21T23:01:21Z","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","publication_identifier":{"isbn":["9788412110104"],"issn":["2518-6582"]},"type":"conference","date_updated":"2023-09-08T11:21:54Z"},{"has_accepted_license":"1","oa":1,"keyword":["Multidisciplinary"],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","type":"journal_article","date_updated":"2021-12-14T07:52:30Z","file_date_updated":"2021-06-04T12:50:47Z","publication":"Proceedings of the National Academy of Sciences","date_created":"2021-06-04T12:38:20Z","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"DaZi"}],"publication_status":"published","day":"07","doi":"10.1073/pnas.1821435116","month":"05","scopus_import":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"date_created":"2021-06-04T12:50:47Z","file_id":"9461","file_name":"2019_PNAS_Kim.pdf","date_updated":"2021-06-04T12:50:47Z","creator":"asandaue","file_size":1142540,"access_level":"open_access","success":1,"content_type":"application/pdf","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","relation":"main_file"}],"citation":{"apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, 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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.","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.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116."},"status":"public","author":[{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"first_name":"Akemi","full_name":"Ono, Akemi","last_name":"Ono"},{"first_name":"Stefan","last_name":"Scholten","full_name":"Scholten, 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","_id":"9460","external_id":{"pmid":["31000601"]},"issue":"19","volume":116,"intvolume":" 116","page":"9652-9657","article_processing_charge":"No","pmid":1,"date_published":"2019-05-07T00:00:00Z","year":"2019","ddc":["580"],"publisher":"National Academy of Sciences"},{"article_processing_charge":"No","pmid":1,"date_published":"2019-10-10T00:00:00Z","year":"2019","article_number":"62","ddc":["570"],"publisher":"Springer Nature","author":[{"first_name":"Keith D.","full_name":"Harris, Keith D.","last_name":"Harris"},{"last_name":"Lloyd","full_name":"Lloyd, James P. B.","first_name":"James P. B."},{"first_name":"Katherine","last_name":"Domb","full_name":"Domb, Katherine"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"last_name":"Zemach","full_name":"Zemach, Assaf","first_name":"Assaf"}],"_id":"9530","extern":"1","external_id":{"pmid":["31601251"]},"volume":12,"intvolume":" 12","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"DaZi"}],"publication_status":"published","day":"10","doi":"10.1186/s13072-019-0307-4","month":"10","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"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.","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.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.","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.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","apa":"Harris, K. D., Lloyd, J. P. B., 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. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","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. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","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,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019."},"file":[{"file_id":"9531","date_created":"2021-06-08T09:29:19Z","file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","date_updated":"2021-06-08T09:29:19Z","file_size":3221067,"creator":"asandaue","success":1,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"86ff50a7517891511af2733c76c81b67"}],"status":"public","has_accepted_license":"1","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","article_type":"original","type":"journal_article","date_updated":"2021-12-14T07:53:00Z","file_date_updated":"2021-06-08T09:29:19Z","date_created":"2021-06-08T09:21:51Z","publication":"Epigenetics and Chromatin","publication_identifier":{"eissn":["1756-8935"]},"abstract":[{"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.","lang":"eng"}]},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.08462"}],"status":"public","citation":{"short":"D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111.","mla":"Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.","chicago":"Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z.","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,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019.","ama":"Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z","apa":"Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z"},"arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","month":"08","publication_status":"published","doi":"10.1007/s11856-019-1897-z","day":"01","type":"journal_article","date_updated":"2023-02-23T14:01:41Z","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."}],"publication":"Israel Journal of Mathematics","date_created":"2021-06-21T13:36:02Z","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"oa":1,"article_type":"original","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Hypergraph cuts above the average","year":"2019","publisher":"Springer","article_processing_charge":"No","page":"67-111","date_published":"2019-08-01T00:00:00Z","volume":233,"intvolume":" 233","author":[{"first_name":"David","last_name":"Conlon","full_name":"Conlon, David"},{"last_name":"Fox","full_name":"Fox, Jacob","first_name":"Jacob"},{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","last_name":"Kwan"},{"first_name":"Benny","last_name":"Sudakov","full_name":"Sudakov, Benny"}],"_id":"9580","external_id":{"arxiv":["1803.08462"]},"extern":"1","issue":"1"},{"oa_version":"Submitted Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"publication_status":"published","doi":"10.1090/tran/7729","day":"15","month":"10","scopus_import":"1","citation":{"ieee":"M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.","apa":"Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729","ama":"Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729","mla":"Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729.","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.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.","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."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1090/tran/7729"}],"oa":1,"title":"Proof of a conjecture on induced subgraphs of Ramsey graphs","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_type":"original","type":"journal_article","date_updated":"2023-02-23T14:01:50Z","date_created":"2021-06-22T09:31:45Z","publication":"Transactions of the American Mathematical Society","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"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."}],"page":"5571-5594","article_processing_charge":"No","date_published":"2019-10-15T00:00:00Z","year":"2019","publisher":"American Mathematical Society","author":[{"last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","orcid":"0000-0002-4003-7567","first_name":"Matthew Alan"},{"first_name":"Benny","full_name":"Sudakov, Benny","last_name":"Sudakov"}],"_id":"9585","issue":"8","extern":"1","external_id":{"arxiv":["1712.05656"]},"volume":372,"intvolume":" 372"},{"page":"757-777","article_processing_charge":"No","date_published":"2019-05-03T00:00:00Z","year":"2019","publisher":"Wiley","author":[{"id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","full_name":"Kwan, Matthew Alan","last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567"},{"full_name":"Sudakov, Benny","last_name":"Sudakov","first_name":"Benny"},{"full_name":"Tran, Tuan","last_name":"Tran","first_name":"Tuan"}],"_id":"9586","external_id":{"arxiv":["1807.05202"]},"issue":"3","extern":"1","volume":99,"intvolume":" 99","quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"arxiv":1,"publication_status":"published","doi":"10.1112/jlms.12192","day":"03","month":"05","scopus_import":"1","citation":{"ista":"Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777.","mla":"Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192.","chicago":"Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192.","short":"M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777.","apa":"Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192","ama":"Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192","ieee":"M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019."},"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1807.05202","open_access":"1"}],"oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Anticoncentration for subgraph statistics","article_type":"original","type":"journal_article","date_updated":"2023-02-23T14:01:53Z","date_created":"2021-06-22T09:46:03Z","publication":"Journal of the London Mathematical Society","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"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"}]},{"main_file_link":[{"url":"https://arxiv.org/abs/1808.03824","open_access":"1"}],"status":"public","citation":{"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.","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.” Computer Physics Communications. Elsevier, 2019. https://doi.org/10.1016/j.cpc.2018.09.020.","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.” Computer Physics Communications, vol. 236, Elsevier, 2019, pp. 214–23, doi:10.1016/j.cpc.2018.09.020.","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. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020","ama":"Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 2019;236:214-223. doi:10.1016/j.cpc.2018.09.020","ieee":"V. Kapil et al., “i-PI 2.0: A universal force engine for advanced molecular simulations,” Computer Physics Communications, vol. 236. Elsevier, pp. 214–223, 2019."},"scopus_import":"1","month":"03","publication_status":"published","doi":"10.1016/j.cpc.2018.09.020","day":"01","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"date_created":"2021-07-16T08:53:01Z","publication":"Computer Physics Communications","publication_identifier":{"issn":["0010-4655"]},"type":"journal_article","date_updated":"2021-08-09T12:37:16Z","article_type":"original","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"i-PI 2.0: A universal force engine for advanced molecular simulations","oa":1,"publisher":"Elsevier","year":"2019","date_published":"2019-03-01T00:00:00Z","article_processing_charge":"No","page":"214-223","intvolume":" 236","volume":236,"extern":"1","_id":"9677","external_id":{"arxiv":["1808.03824"]},"author":[{"first_name":"Venkat","last_name":"Kapil","full_name":"Kapil, Venkat"},{"first_name":"Mariana","full_name":"Rossi, Mariana","last_name":"Rossi"},{"first_name":"Ondrej","last_name":"Marsalek","full_name":"Marsalek, Ondrej"},{"first_name":"Riccardo","full_name":"Petraglia, Riccardo","last_name":"Petraglia"},{"full_name":"Litman, Yair","last_name":"Litman","first_name":"Yair"},{"last_name":"Spura","full_name":"Spura, Thomas","first_name":"Thomas"},{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"full_name":"Cuzzocrea, Alice","last_name":"Cuzzocrea","first_name":"Alice"},{"last_name":"Meißner","full_name":"Meißner, Robert H.","first_name":"Robert H."},{"first_name":"David M.","full_name":"Wilkins, David M.","last_name":"Wilkins"},{"full_name":"Helfrecht, Benjamin A.","last_name":"Helfrecht","first_name":"Benjamin A."},{"last_name":"Juda","full_name":"Juda, Przemysław","first_name":"Przemysław"},{"full_name":"Bienvenue, Sébastien P.","last_name":"Bienvenue","first_name":"Sébastien P."},{"first_name":"Wei","last_name":"Fang","full_name":"Fang, Wei"},{"full_name":"Kessler, Jan","last_name":"Kessler","first_name":"Jan"},{"full_name":"Poltavsky, Igor","last_name":"Poltavsky","first_name":"Igor"},{"first_name":"Steven","full_name":"Vandenbrande, Steven","last_name":"Vandenbrande"},{"first_name":"Jelle","full_name":"Wieme, Jelle","last_name":"Wieme"},{"first_name":"Clemence","last_name":"Corminboeuf","full_name":"Corminboeuf, Clemence"},{"last_name":"Kühne","full_name":"Kühne, Thomas D.","first_name":"Thomas D."},{"last_name":"Manolopoulos","full_name":"Manolopoulos, David E.","first_name":"David E."},{"first_name":"Thomas E.","last_name":"Markland","full_name":"Markland, Thomas E."},{"last_name":"Richardson","full_name":"Richardson, Jeremy O.","first_name":"Jeremy O."},{"full_name":"Tkatchenko, Alexandre","last_name":"Tkatchenko","first_name":"Alexandre"},{"first_name":"Gareth A.","full_name":"Tribello, Gareth A.","last_name":"Tribello"},{"first_name":"Veronique","last_name":"Van Speybroeck","full_name":"Van Speybroeck, Veronique"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}]},{"oa":1,"article_type":"original","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Iterative unbiasing of quasi-equilibrium sampling","date_updated":"2021-08-09T12:37:37Z","type":"journal_article","abstract":[{"text":"Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality.","lang":"eng"}],"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"date_created":"2021-07-19T06:56:45Z","publication":"Journal of Chemical Theory and Computation","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","month":"01","doi":"10.1021/acs.jctc.9b00907","day":"14","publication_status":"published","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.01140"}],"status":"public","citation":{"ista":"Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107.","short":"F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107.","mla":"Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.","chicago":"Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation. American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.","ama":"Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107. doi:10.1021/acs.jctc.9b00907","apa":"Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907","ieee":"F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019."},"author":[{"full_name":"Giberti, F.","last_name":"Giberti","first_name":"F."},{"last_name":"Cheng","full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing"},{"first_name":"G. A.","last_name":"Tribello","full_name":"Tribello, G. A."},{"first_name":"M.","full_name":"Ceriotti, M.","last_name":"Ceriotti"}],"_id":"9680","issue":"1","extern":"1","external_id":{"pmid":["31743021"],"arxiv":["1911.01140"]},"volume":16,"intvolume":" 16","article_processing_charge":"No","page":"100-107","pmid":1,"date_published":"2019-01-14T00:00:00Z","year":"2019","publisher":"American Chemical Society"},{"year":"2019","publisher":"National Academy of Sciences","page":"1110-1115","article_processing_charge":"No","pmid":1,"date_published":"2019-01-22T00:00:00Z","volume":116,"intvolume":" 116","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632"},{"last_name":"Engel","full_name":"Engel, Edgar A.","first_name":"Edgar A."},{"first_name":"Jörg","last_name":"Behler","full_name":"Behler, Jörg"},{"last_name":"Dellago","full_name":"Dellago, Christoph","first_name":"Christoph"},{"first_name":"Michele","last_name":"Ceriotti","full_name":"Ceriotti, Michele"}],"extern":"1","_id":"9689","issue":"4","external_id":{"arxiv":["1811.08630"],"pmid":["30610171"]},"scopus_import":"1","citation":{"ieee":"B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” Proceedings of the National Academy of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019.","apa":"Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116","ama":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 2019;116(4):1110-1115. doi:10.1073/pnas.1815117116","chicago":"Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.","short":"B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115.","mla":"Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.","ista":"Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1815117116"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"doi":"10.1073/pnas.1815117116","day":"22","publication_status":"published","month":"01","date_updated":"2023-02-23T14:05:08Z","type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","date_created":"2021-07-19T10:17:09Z","abstract":[{"lang":"eng","text":"A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water."}],"oa":1,"title":"Ab initio thermodynamics of liquid and solid water","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_type":"original"},{"date_created":"2021-07-27T09:51:46Z","abstract":[{"text":"A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)","lang":"eng"}],"date_updated":"2026-06-18T19:17:32Z","type":"research_data_reference","_id":"9726","title":"Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"},{"first_name":"Reinhard","last_name":"Lipowsky","full_name":"Lipowsky, Reinhard"}],"citation":{"apa":"Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001","ama":"Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001","ieee":"M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019.","ista":"Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001.","chicago":"Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.","mla":"Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.","short":"M.C. Ucar, R. Lipowsky, (2019)."},"publisher":"American Chemical Society ","status":"public","year":"2019","day":"19","doi":"10.1021/acs.nanolett.9b04445.s001","department":[{"_id":"EdHa"}],"date_published":"2019-12-19T00:00:00Z","month":"12","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7166"}]},"oa_version":"Published Version","article_processing_charge":"No"},{"date_updated":"2026-04-03T09:39:40Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. 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