--- _id: '8416' 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. article_processing_charge: No article_type: original author: - first_name: Guan full_name: Huang, Guan last_name: Huang - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: 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 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 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. 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. 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. 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. short: G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327. date_created: 2020-09-17T10:41:36Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T08:19:08Z day: '01' doi: 10.17323/1609-4514-2019-19-2-307-327 extern: '1' external_id: arxiv: - '1809.09341' intvolume: ' 19' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.09341 month: '04' oa: 1 oa_version: Preprint page: 307-327 publication: Moscow Mathematical Journal publication_identifier: issn: - 1609-4514 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '8693' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Luigi full_name: Chierchia, Luigi last_name: Chierchia - first_name: Edmond full_name: Koudjinan, Edmond id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E last_name: Koudjinan orcid: 0000-0003-2640-4049 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 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. 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. date_created: 2020-10-21T15:25:45Z date_published: 2019-12-10T00:00:00Z date_updated: 2021-01-12T08:20:34Z day: '10' doi: 10.1134/S1560354719060017 extern: '1' external_id: arxiv: - '1908.02523' intvolume: ' 24' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.02523 month: '12' oa: 1 oa_version: Preprint page: 583–606 publication: Regular and Chaotic Dynamics publication_status: published publisher: Springer quality_controlled: '1' status: public title: V. I. Arnold’s “pointwise” KAM theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2019' ... --- _id: '9018' 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. article_processing_charge: No article_type: original author: - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Albane full_name: Gaubert, Albane last_name: Gaubert - first_name: Jessica full_name: Andreani, Jessica last_name: Andreani - first_name: Gwenaëlle full_name: Moal, Gwenaëlle last_name: Moal - first_name: Guillaume full_name: Pinna, Guillaume last_name: Pinna - first_name: Ekaterina full_name: Boyarchuk, Ekaterina last_name: Boyarchuk - first_name: Marie-Cécile full_name: Gaillard, Marie-Cécile last_name: Gaillard - first_name: Regis full_name: Courbeyrette, Regis last_name: Courbeyrette - first_name: Carl full_name: Mann, Carl last_name: Mann - first_name: Jean-Yves full_name: Thuret, Jean-Yves last_name: Thuret - first_name: Bérengère full_name: Guichard, Bérengère last_name: Guichard - first_name: Brice full_name: Murciano, Brice last_name: Murciano - 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 - first_name: Marie-Hélène full_name: Le Du, Marie-Hélène last_name: Le Du - first_name: Morgane full_name: Agez, Morgane last_name: Agez - first_name: Caroline full_name: Roelants, Caroline last_name: Roelants - first_name: Zachary A. full_name: Gurard-Levin, Zachary A. last_name: Gurard-Levin - first_name: Geneviève full_name: Almouzni, Geneviève last_name: Almouzni - first_name: Nadia full_name: Cherradi, Nadia last_name: Cherradi - first_name: Raphael full_name: Guerois, Raphael last_name: Guerois - first_name: Françoise full_name: Ochsenbein, Françoise last_name: Ochsenbein citation: 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 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 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. 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. 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.” 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. date_created: 2021-01-19T11:04:50Z date_published: 2019-11-21T00:00:00Z date_updated: 2023-02-23T13:46:53Z day: '21' doi: 10.1016/j.chembiol.2019.09.002 extern: '1' external_id: pmid: - '31543461' intvolume: ' 26' issue: '11' keyword: - Clinical Biochemistry - Molecular Medicine - Biochemistry - Molecular Biology - Pharmacology - Drug Discovery language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.chembiol.2019.09.002 month: '11' oa: 1 oa_version: Published Version page: 1573-1585.e10 pmid: 1 publication: Cell Chemical Biology publication_identifier: issn: - 2451-9456 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2019' ... --- _id: '9530' 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." article_number: '62' article_processing_charge: No article_type: original author: - first_name: Keith D. full_name: Harris, Keith D. last_name: Harris - first_name: James P. B. full_name: Lloyd, James P. B. last_name: Lloyd - first_name: Katherine full_name: Domb, Katherine last_name: Domb - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach citation: 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 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 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. 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. 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.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4. short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019). date_created: 2021-06-08T09:21:51Z date_published: 2019-10-10T00:00:00Z date_updated: 2021-12-14T07:53:00Z day: '10' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13072-019-0307-4 extern: '1' external_id: pmid: - '31601251' file: - access_level: open_access checksum: 86ff50a7517891511af2733c76c81b67 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:29:19Z date_updated: 2021-06-08T09:29:19Z file_id: '9531' file_name: 2019_EpigeneticsAndChromatin_Harris.pdf file_size: 3221067 relation: main_file success: 1 file_date_updated: 2021-06-08T09:29:19Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Epigenetics and Chromatin publication_identifier: eissn: - 1756-8935 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2019' ... --- _id: '9586' abstract: - lang: eng text: "Consider integers \U0001D458,ℓ such that 0⩽ℓ⩽(\U0001D4582) . Given a large graph \U0001D43A , what is the fraction of \U0001D458 -vertex subsets of \U0001D43A \ which span exactly ℓ edges? When \U0001D43A is empty or complete, and ℓ \ is zero or (\U0001D4582) , 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,(\U0001D4582)−ℓ} . Our main result is that for any \U0001D458 and ℓ , the fraction of \U0001D458 -vertex subsets that span ℓ edges is at most log\U0001D442(1)(ℓ∗/\U0001D458)√ \U0001D458/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." article_processing_charge: No article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov - first_name: Tuan full_name: Tran, Tuan last_name: Tran citation: 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 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 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. 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. 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. short: M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777. date_created: 2021-06-22T09:46:03Z date_published: 2019-05-03T00:00:00Z date_updated: 2023-02-23T14:01:53Z day: '03' doi: 10.1112/jlms.12192 extern: '1' external_id: arxiv: - '1807.05202' intvolume: ' 99' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.05202 month: '05' oa: 1 oa_version: Preprint page: 757-777 publication: Journal of the London Mathematical Society publication_identifier: eissn: - 1469-7750 issn: - 0024-6107 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Anticoncentration for subgraph statistics type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 99 year: '2019' ... --- _id: '9580' 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. article_processing_charge: No article_type: original author: - first_name: David full_name: Conlon, David last_name: Conlon - first_name: Jacob full_name: Fox, Jacob last_name: Fox - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: 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 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. 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. ista: Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 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. short: D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111. date_created: 2021-06-21T13:36:02Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-02-23T14:01:41Z day: '01' doi: 10.1007/s11856-019-1897-z extern: '1' external_id: arxiv: - '1803.08462' intvolume: ' 233' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.08462 month: '08' oa: 1 oa_version: Preprint page: 67-111 publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Hypergraph cuts above the average type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 233 year: '2019' ... --- _id: '9585' 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. article_processing_charge: No article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: 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 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 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. 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. 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.” 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. date_created: 2021-06-22T09:31:45Z date_published: 2019-10-15T00:00:00Z date_updated: 2023-02-23T14:01:50Z day: '15' doi: 10.1090/tran/7729 extern: '1' external_id: arxiv: - '1712.05656' intvolume: ' 372' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1090/tran/7729 month: '10' oa: 1 oa_version: Submitted Version page: 5571-5594 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - 1088-6850 issn: - 0002-9947 publication_status: published publisher: American Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Proof of a conjecture on induced subgraphs of Ramsey graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 372 year: '2019' ... --- _id: '9677' 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. article_processing_charge: No article_type: original author: - first_name: Venkat full_name: Kapil, Venkat last_name: Kapil - first_name: Mariana full_name: Rossi, Mariana last_name: Rossi - first_name: Ondrej full_name: Marsalek, Ondrej last_name: Marsalek - first_name: Riccardo full_name: Petraglia, Riccardo last_name: Petraglia - first_name: Yair full_name: Litman, Yair last_name: Litman - first_name: Thomas full_name: Spura, Thomas last_name: Spura - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alice full_name: Cuzzocrea, Alice last_name: Cuzzocrea - first_name: Robert H. full_name: Meißner, Robert H. last_name: Meißner - first_name: David M. full_name: Wilkins, David M. last_name: Wilkins - first_name: Benjamin A. full_name: Helfrecht, Benjamin A. last_name: Helfrecht - first_name: Przemysław full_name: Juda, Przemysław last_name: Juda - first_name: Sébastien P. full_name: Bienvenue, Sébastien P. last_name: Bienvenue - first_name: Wei full_name: Fang, Wei last_name: Fang - first_name: Jan full_name: Kessler, Jan last_name: Kessler - first_name: Igor full_name: Poltavsky, Igor last_name: Poltavsky - first_name: Steven full_name: Vandenbrande, Steven last_name: Vandenbrande - first_name: Jelle full_name: Wieme, Jelle last_name: Wieme - first_name: Clemence full_name: Corminboeuf, Clemence last_name: Corminboeuf - first_name: Thomas D. full_name: Kühne, Thomas D. last_name: Kühne - first_name: David E. full_name: Manolopoulos, David E. last_name: Manolopoulos - first_name: Thomas E. full_name: Markland, Thomas E. last_name: Markland - first_name: Jeremy O. full_name: Richardson, Jeremy O. last_name: Richardson - first_name: Alexandre full_name: Tkatchenko, Alexandre last_name: Tkatchenko - first_name: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Veronique full_name: Van Speybroeck, Veronique last_name: Van Speybroeck - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: 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' 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' 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.' 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.' 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.' 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.' 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. date_created: 2021-07-16T08:53:01Z date_published: 2019-03-01T00:00:00Z date_updated: 2021-08-09T12:37:16Z day: '01' doi: 10.1016/j.cpc.2018.09.020 extern: '1' external_id: arxiv: - '1808.03824' intvolume: ' 236' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.03824 month: '03' oa: 1 oa_version: Preprint page: 214-223 publication: Computer Physics Communications publication_identifier: issn: - 0010-4655 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'i-PI 2.0: A universal force engine for advanced molecular simulations' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 236 year: '2019' ... --- _id: '9680' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: F. full_name: Giberti, F. last_name: Giberti - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: G. A. full_name: Tribello, G. A. last_name: Tribello - first_name: M. full_name: Ceriotti, M. last_name: Ceriotti citation: 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 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. 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. 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. 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. short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107. date_created: 2021-07-19T06:56:45Z date_published: 2019-01-14T00:00:00Z date_updated: 2021-08-09T12:37:37Z day: '14' doi: 10.1021/acs.jctc.9b00907 extern: '1' external_id: arxiv: - '1911.01140' pmid: - '31743021' intvolume: ' 16' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.01140 month: '01' oa: 1 oa_version: Preprint page: 100-107 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Iterative unbiasing of quasi-equilibrium sampling type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 16 year: '2019' ... --- _id: '12600' abstract: - lang: eng text: The snow cover dynamics of High Mountain Asia are usually assessed at spatial resolutions of 250 m or greater, but this scale is too coarse to clearly represent the rugged topography common to the region. Higher-resolution measurement of snow-covered area often results in biased sampling due to cloud cover and deep shadows. We therefore develop a Normalized Difference Snow Index-based workflow to delineate snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning 1999 to 2013. For each scene, we determine the spatial distribution of snow line altitudes (SLAs) with respect to aspect and across six subcatchments. Our results show that the mean SLA exhibits distinct seasonal behavior based on aspect and subcatchment position. We find that SLA dynamics respond to spatial and seasonal trade-offs in precipitation, temperature, and solar radiation, which act as primary controls. We identify two SLA spatial gradients, which we attribute to the effect of spatially variable precipitation. Our results also reveal that aspect-related SLA differences vary seasonally and are influenced by solar radiation. In terms of seasonal dominant controls, we demonstrate that the snow line is controlled by snow precipitation in winter, melt in premonsoon, a combination of both in postmonsoon, and temperature in monsoon, explaining to a large extent the spatial and seasonal variability of the SLA in the upper Langtang Valley. We conclude that while SLA and snow-covered area are complementary metrics, the SLA has a strong potential for understanding local-scale snow cover dynamics and their controlling mechanisms. article_processing_charge: No article_type: original author: - first_name: Marc full_name: Girona‐Mata, Marc last_name: Girona‐Mata - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Silvan full_name: Ragettli, Silvan last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935 apa: Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019). High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2019wr024935 chicago: Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research. American Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935. ieee: M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical Union, pp. 6754–6772, 2019. ista: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 55(8), 6754–6772. mla: Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935. short: M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772. date_created: 2023-02-20T08:12:59Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-02-28T12:14:18Z day: '01' doi: 10.1029/2019wr024935 extern: '1' intvolume: ' 55' issue: '8' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2019WR024935 month: '08' oa: 1 oa_version: Published Version page: 6754-6772 publication: Water Resources Research publication_identifier: eissn: - 1944-7973 issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2019' ...