--- _id: '10128' abstract: - lang: eng text: 'An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand.' acknowledgement: This work has been supported by the MZOŠ projects 098-0352851-2921 and 119-1191342-2959. article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: T. full_name: Hrenar, T. last_name: Hrenar - first_name: M. full_name: Mališ, M. last_name: Mališ - first_name: N. full_name: Došlić, N. last_name: Došlić citation: ama: Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. Physical Chemistry Chemical Physics. 2010;12(18):4678-4685. doi:10.1039/b923041f apa: Šarić, A., Hrenar, T., Mališ, M., & Došlić, N. (2010). Quantum mechanical study of secondary structure formation in protected dipeptides. Physical Chemistry Chemical Physics. Royal Society of Chemistry . https://doi.org/10.1039/b923041f chicago: Šarić, Anđela, T. Hrenar, M. Mališ, and N. Došlić. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” Physical Chemistry Chemical Physics. Royal Society of Chemistry , 2010. https://doi.org/10.1039/b923041f. ieee: A. Šarić, T. Hrenar, M. Mališ, and N. Došlić, “Quantum mechanical study of secondary structure formation in protected dipeptides,” Physical Chemistry Chemical Physics, vol. 12, no. 18. Royal Society of Chemistry , pp. 4678–4685, 2010. ista: Šarić A, Hrenar T, Mališ M, Došlić N. 2010. Quantum mechanical study of secondary structure formation in protected dipeptides. Physical Chemistry Chemical Physics. 12(18), 4678–4685. mla: Šarić, Anđela, et al. “Quantum Mechanical Study of Secondary Structure Formation in Protected Dipeptides.” Physical Chemistry Chemical Physics, vol. 12, no. 18, Royal Society of Chemistry , 2010, pp. 4678–85, doi:10.1039/b923041f. short: A. Šarić, T. Hrenar, M. Mališ, N. Došlić, Physical Chemistry Chemical Physics 12 (2010) 4678–4685. date_created: 2021-10-12T08:44:34Z date_published: 2010-03-16T00:00:00Z date_updated: 2021-10-12T09:49:22Z day: '16' doi: 10.1039/b923041f extern: '1' external_id: pmid: - '20428547' intvolume: ' 12' issue: '18' keyword: - Physical and Theoretical Chemistry - General Physics and Astronomy language: - iso: eng main_file_link: - url: https://europepmc.org/article/med/20428547 month: '03' oa_version: None page: 4678-4685 pmid: 1 publication: Physical Chemistry Chemical Physics publication_identifier: issn: - 1463-9076 - 1463-9084 publication_status: published publisher: 'Royal Society of Chemistry ' quality_controlled: '1' status: public title: Quantum mechanical study of secondary structure formation in protected dipeptides type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2010' ... --- _id: '10127' abstract: - lang: eng text: We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies for helpful discussions. article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Particle self-assembly on soft elastic shells. Soft Matter. 2010;7(5):1874-1878. doi:10.1039/c0sm01143f apa: Šarić, A., & Cacciuto, A. (2010). Particle self-assembly on soft elastic shells. Soft Matter. Royal Society of Chemistry (RSC). https://doi.org/10.1039/c0sm01143f chicago: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” Soft Matter. Royal Society of Chemistry (RSC), 2010. https://doi.org/10.1039/c0sm01143f. ieee: A. Šarić and A. Cacciuto, “Particle self-assembly on soft elastic shells,” Soft Matter, vol. 7, no. 5. Royal Society of Chemistry (RSC), pp. 1874–1878, 2010. ista: Šarić A, Cacciuto A. 2010. Particle self-assembly on soft elastic shells. Soft Matter. 7(5), 1874–1878. mla: Šarić, Anđela, and Angelo Cacciuto. “Particle Self-Assembly on Soft Elastic Shells.” Soft Matter, vol. 7, no. 5, Royal Society of Chemistry (RSC), 2010, pp. 1874–78, doi:10.1039/c0sm01143f. short: A. Šarić, A. Cacciuto, Soft Matter 7 (2010) 1874–1878. date_created: 2021-10-12T08:34:23Z date_published: 2010-12-23T00:00:00Z date_updated: 2021-10-12T09:49:27Z day: '23' doi: 10.1039/c0sm01143f extern: '1' external_id: arxiv: - '1010.2453' intvolume: ' 7' issue: '5' keyword: - condensed matter physics - general chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1010.2453 month: '12' oa: 1 oa_version: Preprint page: 1874-1878 publication: Soft Matter publication_identifier: issn: - 1744-683X - 1744-6848 publication_status: published publisher: Royal Society of Chemistry (RSC) quality_controlled: '1' status: public title: Particle self-assembly on soft elastic shells type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 7 year: '2010' ... --- _id: '10390' abstract: - lang: eng text: 'We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases, which includes most of the mesophases observed in self-assembly of block copolymers but also crystalline structures formed by asymmetric, hard binary mixtures. Our results detail the phenomenological behavior of these systems when softness is introduced in terms of two different classes of interparticle interactions: (a) the elastic Hertz potential, which has a finite energy cost for complete overlap of any two components, and (b) a generic power-law repulsion with tunable exponent. We discuss how simple geometric arguments can be used to account for the large structural variety observed in these systems and detail the similarities and differences in the phase behavior for the two classes of potentials under consideration.' acknowledgement: This work was supported by the National Science Foundation under CAREER Grant No. DMR-0846426 and partly by Columbia University. article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Behnaz full_name: Bozorgui, Behnaz last_name: Bozorgui - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Bozorgui B, Cacciuto A. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 2010;115(22):7182-7189. doi:10.1021/jp107545w apa: Šarić, A., Bozorgui, B., & Cacciuto, A. (2010). Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/jp107545w chicago: Šarić, Anđela, Behnaz Bozorgui, and Angelo Cacciuto. “Packing of Soft Asymmetric Dumbbells.” The Journal of Physical Chemistry B. American Chemical Society, 2010. https://doi.org/10.1021/jp107545w. ieee: A. Šarić, B. Bozorgui, and A. Cacciuto, “Packing of soft asymmetric dumbbells,” The Journal of Physical Chemistry B, vol. 115, no. 22. American Chemical Society, pp. 7182–7189, 2010. ista: Šarić A, Bozorgui B, Cacciuto A. 2010. Packing of soft asymmetric dumbbells. The Journal of Physical Chemistry B. 115(22), 7182–7189. mla: Šarić, Anđela, et al. “Packing of Soft Asymmetric Dumbbells.” The Journal of Physical Chemistry B, vol. 115, no. 22, American Chemical Society, 2010, pp. 7182–89, doi:10.1021/jp107545w. short: A. Šarić, B. Bozorgui, A. Cacciuto, The Journal of Physical Chemistry B 115 (2010) 7182–7189. date_created: 2021-11-29T15:13:17Z date_published: 2010-10-15T00:00:00Z date_updated: 2021-11-29T16:20:29Z day: '15' doi: 10.1021/jp107545w extern: '1' external_id: arxiv: - '1010.2458' pmid: - '20949934' intvolume: ' 115' issue: '22' keyword: - materials chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1010.2458 month: '10' oa: 1 oa_version: Preprint page: 7182-7189 pmid: 1 publication: The Journal of Physical Chemistry B publication_identifier: eissn: - 1520-5207 issn: - 1520-6106 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Packing of soft asymmetric dumbbells type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 115 year: '2010' ... --- _id: '10391' abstract: - lang: eng text: We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results. acknowledgement: This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. article_number: '226101' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Josep C. full_name: Pàmies, Josep C. last_name: Pàmies - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Pàmies JC, Cacciuto A. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. Physical Review Letters. 2010;104(22). doi:10.1103/physrevlett.104.226101 apa: Šarić, A., Pàmies, J. C., & Cacciuto, A. (2010). Effective elasticity of a flexible filament bound to a deformable cylindrical surface. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.226101 chicago: Šarić, Anđela, Josep C. Pàmies, and Angelo Cacciuto. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” Physical Review Letters. American Physical Society, 2010. https://doi.org/10.1103/physrevlett.104.226101. ieee: A. Šarić, J. C. Pàmies, and A. Cacciuto, “Effective elasticity of a flexible filament bound to a deformable cylindrical surface,” Physical Review Letters, vol. 104, no. 22. American Physical Society, 2010. ista: Šarić A, Pàmies JC, Cacciuto A. 2010. Effective elasticity of a flexible filament bound to a deformable cylindrical surface. Physical Review Letters. 104(22), 226101. mla: Šarić, Anđela, et al. “Effective Elasticity of a Flexible Filament Bound to a Deformable Cylindrical Surface.” Physical Review Letters, vol. 104, no. 22, 226101, American Physical Society, 2010, doi:10.1103/physrevlett.104.226101. short: A. Šarić, J.C. Pàmies, A. Cacciuto, Physical Review Letters 104 (2010). date_created: 2021-11-29T15:14:33Z date_published: 2010-06-03T00:00:00Z date_updated: 2021-11-30T08:11:19Z day: '03' doi: 10.1103/physrevlett.104.226101 extern: '1' external_id: arxiv: - '1005.2429' pmid: - '20867183' intvolume: ' 104' issue: '22' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1005.2429 month: '06' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Effective elasticity of a flexible filament bound to a deformable cylindrical surface type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 104 year: '2010' ... --- _id: '1042' abstract: - lang: eng text: Recent years have seen tremendous progress in the field of cold and ultracold molecules. A central goal in the field is currently the realization of stable rovibronic ground-state molecular samples in the regime of quantum degeneracy, e.g. in the form of molecular Bose-Einstein condensates, molecular degenerate Fermi gases, or, when an optical lattice is present, molecular Mott-insulator phases. However, molecular samples are not readily cooled to the extremely low temperatures at which quantum degeneracy occurs. In particular, laser cooling, the \'workhorse\' for the field of atomic quantum gases, is generally not applicable to molecular samples. Here we take an important step beyond previous work1 and provide details on the realization of an ultracold quantum gas of ground-state dimer molecules trapped in an optical lattice as recently reported in Ref. 2. We demonstrate full control over all internal and external quantum degrees of freedom for the ground-state molecules by deterministically preparing the molecules in a single quantum state, i.e. in a specific hyperfine sublevel of the rovibronic ground state, while the molecules are trapped in the motional ground state of the individual lattice wells. We circumvent the problem of cooling by associating weakly-bound molecules out of a zero-temperature atomic Mott-insulator state and by transferring these to the absolute ground state in a four-photon STIRAP process. Our preparation procedure directly leads to a long-lived, lattice-trapped molecular many-body state, which we expect to form the platform for many of the envisioned future experiments with molecular quantum gases, e.g. on precision molecular spectroscopy, quantum information science, and dipolar quantum systems. article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Mattias full_name: Gustavsson, Mattias last_name: Gustavsson - first_name: Russell full_name: Hart, Russell last_name: Hart - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: 'Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. In: World Scientific Publishing; 2010:256-269. doi:10.1142/9789814282345_0024' apa: 'Danzl, J. G., Mark, M., Haller, E., Gustavsson, M., Hart, R., & Nägerl, H. (2010). Production of a quantum gas of rovibronic ground-state molecules in an optical lattice (pp. 256–269). Presented at the ICOLS: International Conference on Laser Spectroscopy, World Scientific Publishing. https://doi.org/10.1142/9789814282345_0024' chicago: Danzl, Johann G, Manfred Mark, Elmar Haller, Mattias Gustavsson, Russell Hart, and Hanns Nägerl. “Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice,” 256–69. World Scientific Publishing, 2010. https://doi.org/10.1142/9789814282345_0024. ieee: 'J. G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, and H. Nägerl, “Production of a quantum gas of rovibronic ground-state molecules in an optical lattice,” presented at the ICOLS: International Conference on Laser Spectroscopy, 2010, pp. 256–269.' ista: 'Danzl JG, Mark M, Haller E, Gustavsson M, Hart R, Nägerl H. 2010. Production of a quantum gas of rovibronic ground-state molecules in an optical lattice. ICOLS: International Conference on Laser Spectroscopy, 256–269.' mla: Danzl, Johann G., et al. Production of a Quantum Gas of Rovibronic Ground-State Molecules in an Optical Lattice. World Scientific Publishing, 2010, pp. 256–69, doi:10.1142/9789814282345_0024. short: J.G. Danzl, M. Mark, E. Haller, M. Gustavsson, R. Hart, H. Nägerl, in:, World Scientific Publishing, 2010, pp. 256–269. conference: name: 'ICOLS: International Conference on Laser Spectroscopy' date_created: 2018-12-11T11:49:50Z date_published: 2010-01-01T00:00:00Z date_updated: 2021-01-12T06:47:52Z day: '01' doi: 10.1142/9789814282345_0024 extern: '1' language: - iso: eng month: '01' oa_version: None page: 256 - 269 publication_status: published publisher: World Scientific Publishing publist_id: '6346' status: public title: Production of a quantum gas of rovibronic ground-state molecules in an optical lattice type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2010' ...